Variant report

Variant	rs6838561
Chromosome Location	chr4:1380033-1380034
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:1377040..1378598-chr4:1379053..1381982,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10016557	0.91[CEU][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10023473	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1137789	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11727297	0.96[CEU][hapmap]
rs13123016	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1680080	0.88[CEU][hapmap]
rs1680083	0.88[CEU][hapmap]
rs1732103	0.96[CEU][hapmap]
rs1882098	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1882105	0.82[JPT][hapmap]
rs2141654	0.88[CEU][hapmap]
rs2336081	0.95[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28522910	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28614045	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28733902	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2878607	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4974554	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4974556	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4974606	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4974611	0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4974612	0.96[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4974613	0.87[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4974614	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974616	0.81[ASN][1000 genomes]
rs4974617	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4974618	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4974620	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6599308	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6599309	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6856550	0.86[EUR][1000 genomes]
rs7657357	0.85[EUR][1000 genomes]
rs7664763	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7681872	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7684445	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7688922	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs9328733	0.84[ASN][1000 genomes]
rs9683830	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9996817	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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	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
5	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
6	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
7	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
8	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
9	nsv878340	chr4:1277826-1386570	Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	nsv878341	chr4:1277826-1391400	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv1002635	chr4:1282603-1402761	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer 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	37 gene(s)	inside rSNPs	diseases
12	nsv878343	chr4:1291337-1391400	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv878344	chr4:1291337-1414684	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
14	nsv878345	chr4:1291337-1563920	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
15	nsv878347	chr4:1300077-1866358	Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription 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	69 gene(s)	inside rSNPs	diseases
16	nsv878348	chr4:1305269-1386570	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
17	esv1794294	chr4:1307119-1817474	Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
18	nsv878350	chr4:1320023-1500753	Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
19	nsv878351	chr4:1329847-1414684	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
20	nsv1008785	chr4:1335089-1518521	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
21	nsv536988	chr4:1335089-1518521	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Genic enhancers 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	30 gene(s)	inside rSNPs	diseases
22	nsv593302	chr4:1338618-1414684	ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
23	esv1826930	chr4:1373206-1399091	Bivalent Enhancer Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
24	esv1851616	chr4:1373206-1399091	Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
25	nsv870062	chr4:1376068-1523451	Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
26	esv3340143	chr4:1377502-1380300	Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6838561	MGC21675	cis	multi-tissue	Pritchard
rs6838561	UVSSA	cis	Skin Sun Exposed Lower leg	GTEx
rs6838561	CTBP1	Cis_1M	lymphoblastoid	RTeQTL
rs6838561	KIAA1530	cis	multi-tissue	Pritchard
rs6838561	CRIPAK	cis	Thyroid	GTEx
rs6838561	UVSSA	cis	Nerve Tibial	GTEx
rs6838561	UVSSA	cis	Whole Blood	GTEx
rs6838561	UVSSA	cis	Stomach	GTEx
rs6838561	CTBP1-AS2	cis	Thyroid	GTEx
rs6838561	UVSSA	cis	Esophagus Mucosa	GTEx
rs6838561	UVSSA	cis	lung	GTEx
rs6838561	CRIPAK	cis	multi-tissue	Pritchard
rs6838561	UVSSA	cis	Thyroid	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1341800-1387800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:1341800-1388800	Weak transcription	Small Intestine	intestine
3	chr4:1342200-1382600	Weak transcription	Primary B cells from cord blood	blood
4	chr4:1342600-1385600	Weak transcription	Fetal Kidney	kidney
5	chr4:1342800-1381200	Strong transcription	Fetal Intestine Small	intestine
6	chr4:1343400-1381200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:1346000-1386600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr4:1346000-1389200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:1352600-1382000	Weak transcription	Fetal Brain Male	brain
10	chr4:1353400-1382000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:1353600-1382200	Weak transcription	Osteobl	bone
12	chr4:1355400-1380800	Strong transcription	Fetal Stomach	stomach
13	chr4:1358600-1381200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:1360800-1389600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:1363000-1380400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:1363000-1380800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:1363800-1380400	Strong transcription	Right Ventricle	heart
18	chr4:1364200-1381600	Strong transcription	Ovary	ovary
19	chr4:1368200-1380800	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:1368800-1389200	Weak transcription	NHDF-Ad	bronchial
21	chr4:1370200-1381400	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr4:1370600-1382400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr4:1371400-1382200	Weak transcription	HSMM	muscle
24	chr4:1372400-1380400	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:1373200-1381200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:1374000-1380400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:1374000-1381400	Strong transcription	Placenta Amnion	Placenta Amnion
28	chr4:1374000-1381800	Strong transcription	Placenta	Placenta
29	chr4:1374200-1381600	Strong transcription	Liver	Liver
30	chr4:1374200-1382200	Strong transcription	Adipose Nuclei	Adipose
31	chr4:1374400-1381600	Strong transcription	Primary T cells from cord blood	blood
32	chr4:1374600-1381400	Strong transcription	Aorta	Aorta
33	chr4:1374600-1381600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:1374600-1383000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:1374800-1380800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr4:1375800-1380400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr4:1375800-1382400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr4:1376200-1380800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr4:1376400-1380200	Strong transcription	Fetal Muscle Leg	muscle
40	chr4:1376400-1381000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr4:1376400-1381600	Strong transcription	Esophagus	oesophagus
42	chr4:1376600-1380400	Strong transcription	Gastric	stomach
43	chr4:1376600-1381400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:1376800-1380800	Strong transcription	Fetal Brain Female	brain
45	chr4:1376800-1381600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr4:1376800-1381800	Strong transcription	Brain Hippocampus Middle	brain
47	chr4:1377000-1381200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr4:1377000-1381400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr4:1377000-1381800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr4:1377200-1380600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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