Variant report

Variant	rs2199956
Chromosome Location	chr4:1248919-1248920
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:1236833..1250005-chr4:1276188..1292579,54	MCF-7	breast:
2	chr4:1236808..1249320-chr4:1336333..1343819,66	MCF-7	breast:
3	chr4:1235141..1249133-chr4:1336906..1347308,118	MCF-7	breast:
4	chr4:1238004..1248980-chr4:1275065..1286840,30	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C4orf42-1	chr4:1244047-1249698	ENSG00000196810.4

Variant related genes	Relation type
ENSG00000163945	Chromatin interaction
ENSG00000090316	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11247983	0.85[CEU][hapmap]
rs1128427	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs11721789	0.80[EUR][1000 genomes]
rs11727167	0.85[CEU][hapmap];0.87[TSI][hapmap]
rs11727987	0.80[EUR][1000 genomes]
rs12499546	0.80[EUR][1000 genomes]
rs12502916	0.85[CEU][hapmap]
rs12505362	0.80[EUR][1000 genomes]
rs12506095	0.80[EUR][1000 genomes]
rs12508446	0.84[CEU][hapmap]
rs12641735	1.00[CEU][hapmap]
rs12642410	0.85[CEU][hapmap]
rs12642797	0.80[EUR][1000 genomes]
rs13106092	0.80[EUR][1000 genomes]
rs13110563	0.80[EUR][1000 genomes]
rs13112706	0.85[CEU][hapmap]
rs13115355	0.80[EUR][1000 genomes]
rs13117476	0.86[CHB][hapmap]
rs13124876	0.80[EUR][1000 genomes]
rs13128045	0.85[CEU][hapmap]
rs13132584	0.80[EUR][1000 genomes]
rs13134106	0.85[CEU][hapmap]
rs13148614	0.95[EUR][1000 genomes]
rs13149575	0.85[CEU][hapmap];0.87[TSI][hapmap]
rs13149790	0.80[EUR][1000 genomes]
rs13149952	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs13150571	0.85[CEU][hapmap]
rs1316393	0.81[CEU][hapmap]
rs1680073	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1680074	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1732100	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1732107	0.85[CEU][hapmap]
rs1960426	0.83[TSI][hapmap]
rs2141656	0.86[CHB][hapmap]
rs2291199	0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs3755920	1.00[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs3915420	0.80[EUR][1000 genomes]
rs4246685	0.85[CEU][hapmap]
rs4405964	0.85[CEU][hapmap]
rs4428235	0.85[CEU][hapmap]
rs4493483	0.85[CEU][hapmap]
rs4516656	0.85[CEU][hapmap]
rs4519749	0.85[CEU][hapmap]
rs4642180	0.85[CEU][hapmap]
rs4974542	0.80[EUR][1000 genomes]
rs4974543	0.80[EUR][1000 genomes]
rs4974544	0.80[EUR][1000 genomes]
rs4974575	0.95[EUR][1000 genomes]
rs4974582	0.84[CEU][hapmap]
rs4974594	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs7664474	0.86[CHB][hapmap]
rs7673398	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs7695691	1.00[CEU][hapmap]
rs900027	0.85[CEU][hapmap]
rs900028	0.85[CEU][hapmap]
rs922698	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs9631804	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv829835	chr4:1097586-1304239	Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv878328	chr4:1141573-1990425	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
6	nsv878329	chr4:1147407-1254930	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv878330	chr4:1147407-1523930	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv878331	chr4:1159680-1254930	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv461152	chr4:1159680-1415698	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
10	nsv593278	chr4:1159680-1415698	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
11	nsv461153	chr4:1174861-1254930	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
12	nsv593279	chr4:1174861-1254930	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
13	nsv461154	chr4:1179213-1254930	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
14	nsv593280	chr4:1179213-1254930	Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
15	nsv878332	chr4:1179213-1254930	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
16	nsv997971	chr4:1191256-1518521	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
17	nsv878333	chr4:1193832-1254930	Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
18	nsv461155	chr4:1203265-1352685	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
19	nsv593281	chr4:1203265-1352685	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
20	nsv1002097	chr4:1212573-1320086	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
21	nsv536986	chr4:1212573-1320086	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
22	esv1811773	chr4:1228251-1287474	ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
23	esv1800629	chr4:1228451-1287274	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
24	esv1812851	chr4:1228451-1287274	Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
25	esv1823612	chr4:1228451-1287274	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
26	esv1825633	chr4:1228451-1287274	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
27	esv1838677	chr4:1231540-1274734	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
28	nsv878334	chr4:1232910-1254930	Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
29	esv1839490	chr4:1237014-1254930	Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
30	nsv878335	chr4:1237014-1254930	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
31	nsv878336	chr4:1238859-1254930	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
32	nsv878337	chr4:1240091-1254930	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
33	esv1837491	chr4:1241969-1259650	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
34	nsv593298	chr4:1244267-1342521	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2199956	MAEA	cis	Thyroid	GTEx
rs2199956	CTBP1	cis	multi-tissue	Pritchard
rs2199956	CRIPAK	cis	Thyroid	GTEx
rs2199956	CRIPAK	cis	parietal	SCAN
rs2199956	CTBP1	Cis_1M	lymphoblastoid	RTeQTL
rs2199956	KIAA1530	cis	multi-tissue	Pritchard
rs2199956	KIAA1530	cis	parietal	SCAN
rs2199956	CRIPAK	cis	cerebellum	SCAN
rs2199956	UVSSA	cis	Skin Sun Exposed Lower leg	GTEx
rs2199956	C4orf42	cis	cerebellum	SCAN
rs2199956	KIAA1530	cis	cerebellum	SCAN
rs2199956	MAEA	cis	cerebellum	SCAN
rs2199956	MAEA	cis	Nerve Tibial	GTEx
rs2199956	UVSSA	cis	Whole Blood	GTEx
rs2199956	UVSSA	cis	Stomach	GTEx
rs2199956	ADD1	cis	cerebellum	SCAN
rs2199956	UVSSA	cis	Thyroid	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1244200-1249200	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr4:1244200-1249400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr4:1244200-1249800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr4:1244400-1249000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:1244600-1249200	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr4:1244800-1250400	Weak transcription	Psoas Muscle	Psoas
7	chr4:1245000-1249000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr4:1245400-1258400	Weak transcription	Ovary	ovary
9	chr4:1245400-1282400	Weak transcription	Brain Angular Gyrus	brain
10	chr4:1245600-1266800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:1245800-1249400	Enhancers	Primary T cells fromperipheralblood	blood
12	chr4:1245800-1261800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:1245800-1278600	Weak transcription	Gastric	stomach
14	chr4:1245800-1282600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:1245800-1282600	Weak transcription	Right Ventricle	heart
16	chr4:1246000-1282600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr4:1246400-1249600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:1246600-1249600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr4:1246800-1249200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr4:1247000-1249400	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr4:1247000-1256000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr4:1247400-1254000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr4:1247400-1254200	Weak transcription	Spleen	Spleen
24	chr4:1247400-1263000	Weak transcription	Brain Hippocampus Middle	brain
25	chr4:1247800-1249000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr4:1247800-1254600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:1247800-1258800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr4:1248000-1249600	Weak transcription	Esophagus	oesophagus
29	chr4:1248200-1250000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr4:1248400-1261200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:1248600-1249000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:1248800-1260800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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