Variant report

Variant	rs6537402
Chromosome Location	chr4:147116864-147116865
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:147111066..147113636-chr4:147115907..147120334,4	K562	blood:
2	chr4:147111066..147113405-chr4:147115907..147118837,2	K562	blood:
3	chr4:147116009..147117870-chr4:147118795..147120333,2	MCF-7	breast:
4	chr4:147116335..147119084-chr4:147119994..147121504,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10519776	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1079476	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11100919	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11721367	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11721873	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11723069	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11728609	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11729787	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11730306	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11733347	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11940961	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs12152657	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12152692	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12152709	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17021106	0.83[EUR][1000 genomes]
rs17021186	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17021217	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17021241	0.86[CEU][hapmap]
rs17756234	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs17757522	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17757685	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17757715	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17758092	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17758396	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17758420	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17814023	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17814065	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17814503	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17814598	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1864371	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs1865531	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1865532	0.85[EUR][1000 genomes]
rs2068009	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2115796	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2115797	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2163171	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2164280	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28420466	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3733458	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3733459	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3733460	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3756081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3756082	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3756083	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775498	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3815967	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4282199	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4835286	0.88[CEU][hapmap];0.82[CHB][hapmap];0.83[MEX][hapmap]
rs55736910	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56279747	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56333123	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56393662	0.94[ASN][1000 genomes]
rs62326797	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62326801	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62326802	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62326804	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62326848	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537401	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537403	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6815527	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6816161	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6820462	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6821066	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6821444	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6821479	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6821863	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6824313	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6838458	0.81[EUR][1000 genomes]
rs6839123	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6839141	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6844381	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6856647	0.80[EUR][1000 genomes]
rs6858813	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72727944	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72727952	0.94[ASN][1000 genomes]
rs7657269	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7665079	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7745	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs919482	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs919483	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9308199	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461674	chr4:147047072-147143572	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv595650	chr4:147047072-147143572	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1018859	chr4:147055618-147138397	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv461675	chr4:147116864-147768206	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv595651	chr4:147116864-147768206	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6537402	RP11-6L6.2	cis	Nerve Tibial	GTEx
rs6537402	RP11-6L6.2	cis	Artery Tibial	GTEx
rs6537402	RP11-6L6.2	cis	lung	GTEx
rs6537402	LSM6	cis	parietal	SCAN
rs6537402	RP11-6L6.2	cis	Whole Blood	GTEx
rs6537402	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs6537402	LSM6	cis	cerebellum	SCAN
rs6537402	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147098400-147118600	Weak transcription	Colonic Mucosa	Colon
2	chr4:147103800-147117400	Strong transcription	Primary T cells from cord blood	blood
3	chr4:147109000-147123000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr4:147109800-147126000	Weak transcription	Aorta	Aorta
5	chr4:147111800-147117000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:147112000-147117000	Weak transcription	Ovary	ovary
7	chr4:147112000-147127200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr4:147112200-147117000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr4:147112200-147118400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr4:147112200-147124800	Weak transcription	Spleen	Spleen
11	chr4:147112200-147125200	Weak transcription	Pancreas	Pancrea
12	chr4:147112800-147117000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:147112800-147127600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr4:147113000-147117000	Weak transcription	HSMMtube	muscle
15	chr4:147113200-147123000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:147113200-147124200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr4:147113400-147124400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr4:147113600-147121400	Weak transcription	Primary B cells from cord blood	blood
19	chr4:147113800-147117000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr4:147113800-147117400	Weak transcription	Placenta	Placenta
21	chr4:147113800-147117600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:147113800-147117800	Weak transcription	Fetal Thymus	thymus
23	chr4:147113800-147118200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:147113800-147118800	Weak transcription	Thymus	Thymus
25	chr4:147113800-147124400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr4:147113800-147126400	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr4:147113800-147127400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr4:147114000-147117000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:147114000-147118000	Weak transcription	HSMM	muscle
30	chr4:147114000-147118600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr4:147114000-147120400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr4:147114000-147122000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr4:147114000-147123600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr4:147114000-147125200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr4:147114000-147126000	Weak transcription	Liver	Liver
36	chr4:147114000-147126000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:147114000-147127600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:147114000-147129200	Weak transcription	Brain Hippocampus Middle	brain
39	chr4:147114000-147132600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr4:147114000-147144800	Weak transcription	Gastric	stomach
41	chr4:147114200-147118000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr4:147114200-147118800	Weak transcription	Fetal Muscle Leg	muscle
43	chr4:147114200-147126000	Weak transcription	Adipose Nuclei	Adipose
44	chr4:147114400-147124000	Weak transcription	GM12878-XiMat	blood
45	chr4:147114600-147125400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:147116000-147117800	Enhancers	NH-A	brain
47	chr4:147116200-147117800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:147116400-147117200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:147116400-147117600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:147116400-147117600	Enhancers	NHDF-Ad	bronchial

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