Variant report

Variant	rs877987
Chromosome Location	chr4:1204829-1204830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:1203745-1205221	K562	blood:	n/a	n/a
2	POLR2A	chr4:1204537-1205163	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:1203211-1205143	K562	blood:	n/a	n/a
4	POLR2A	chr4:1204031-1204933	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr4:1204779-1205161	GM12878	blood:	n/a	n/a
6	POLR2A	chr4:1204239-1205131	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:1204715-1205279	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:1204770-1204860	A549	lung:	n/a	n/a
9	POLR2A	chr4:1203482-1205270	HL-60	blood:	n/a	n/a
10	POLR2A	chr4:1204674-1205176	HL-60	blood:	n/a	n/a
11	POLR2A	chr4:1203561-1205231	K562	blood:	n/a	n/a
12	POLR2A	chr4:1204696-1205239	K562	blood:	n/a	n/a
13	POLR2A	chr4:1204691-1205110	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:1204791..1207603-chr4:1281765..1283856,2	MCF-7	breast:
2	chr4:1198351..1202176-chr4:1203916..1208029,5	K562	blood:
3	chr4:1204218..1206634-chr4:1220495..1222901,2	MCF-7	breast:
4	chr4:1199380..1201260-chr4:1203296..1206173,2	MCF-7	breast:
5	chr4:1203383..1207466-chr4:1208474..1210757,3	K562	blood:

No data

Variant related genes	Relation type
SPON2	TF binding region
ENSG00000159692	Chromatin interaction
ENSG00000159674	Chromatin interaction
ENSG00000090316	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1009901	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17164549	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17164680	0.88[JPT][hapmap];1.00[MEX][hapmap]
rs2011161	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2178443	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2279280	0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs3729593	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3733340	0.86[ASW][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.82[MKK][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3755919	0.87[ASN][1000 genomes]
rs3755931	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[ASN][1000 genomes]
rs3755936	0.86[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3755937	0.82[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3755943	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3755950	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3775106	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3775109	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3811733	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs3892033	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55877603	0.85[ASN][1000 genomes]
rs57276390	0.85[ASN][1000 genomes]
rs57560821	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57890261	0.89[ASN][1000 genomes]
rs59717591	0.85[ASN][1000 genomes]
rs60846075	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61010940	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6840663	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6856873	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73069911	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73793112	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73793144	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73793145	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73793148	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73793154	0.90[ASN][1000 genomes]
rs73793165	0.87[ASN][1000 genomes]
rs73793175	0.85[ASN][1000 genomes]
rs900030	0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	nsv1009619	chr4:901897-1215657	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	nsv593276	chr4:1159680-1227469	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv461151	chr4:1159680-1236840	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv593277	chr4:1159680-1236840	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs877987	KIAA1530	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1194200-1207800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:1195200-1214600	Weak transcription	A549	lung
3	chr4:1196400-1209800	Weak transcription	Primary B cells from cord blood	blood
4	chr4:1198000-1211200	Genic enhancers	Fetal Stomach	stomach
5	chr4:1198200-1205200	Enhancers	Stomach Mucosa	stomach
6	chr4:1198400-1207000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:1199000-1205800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:1199200-1207600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr4:1200000-1205200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:1200400-1206200	Enhancers	Ovary	ovary
11	chr4:1200400-1206400	Genic enhancers	Brain Germinal Matrix	brain
12	chr4:1200600-1205800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:1201000-1205000	Enhancers	Fetal Lung	lung
14	chr4:1201000-1205200	Strong transcription	Fetal Brain Female	brain
15	chr4:1201200-1205200	Genic enhancers	Spleen	Spleen
16	chr4:1201400-1205000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:1201400-1206000	Enhancers	NHDF-Ad	bronchial
18	chr4:1201600-1205000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:1201600-1205000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:1201600-1205000	Enhancers	Right Atrium	heart
21	chr4:1201600-1205200	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr4:1201600-1211600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:1201800-1205000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr4:1201800-1209000	Strong transcription	Fetal Thymus	thymus
25	chr4:1201800-1210000	Strong transcription	Thymus	Thymus
26	chr4:1202000-1205200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:1202200-1206000	Weak transcription	HepG2	liver
28	chr4:1202200-1209000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:1202400-1206000	Genic enhancers	Lung	lung
30	chr4:1202400-1207000	Genic enhancers	Gastric	stomach
31	chr4:1202400-1208000	Genic enhancers	Pancreas	Pancrea
32	chr4:1202400-1210000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr4:1202600-1206400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:1202600-1210200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr4:1202800-1205200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr4:1202800-1210200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr4:1202800-1218000	Weak transcription	Fetal Brain Male	brain
38	chr4:1203000-1205200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:1203000-1205200	Genic enhancers	Right Ventricle	heart
40	chr4:1203000-1207200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
41	chr4:1203000-1209600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr4:1203000-1210200	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr4:1203200-1206000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr4:1203200-1206600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr4:1203200-1217800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr4:1203400-1205200	Genic enhancers	Duodenum Mucosa	Duodenum
47	chr4:1203400-1205400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:1203400-1206200	Weak transcription	HUVEC	blood vessel
49	chr4:1203400-1207400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr4:1203400-1209200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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