Variant report

Variant	rs6587638
Chromosome Location	chr1:151938138-151938139
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151937625..151940407-chr1:151960051..151962208,2	K562	blood:
2	chr1:151932606..151935514-chr1:151936511..151938848,2	MCF-7	breast:
3	chr1:149857621..149859138-chr1:151936767..151938512,2	MCF-7	breast:
4	chr1:151881894..151884208-chr1:151935307..151938264,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184678	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1038747	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs10494270	0.89[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs11204919	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204920	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204922	0.85[CHB][hapmap]
rs11582739	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12083193	0.95[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12095483	0.90[ASN][1000 genomes]
rs12116923	0.80[CHB][hapmap]
rs16833668	0.90[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16833669	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16833670	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16833728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16833743	0.95[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1844543	0.88[ASN][1000 genomes]
rs1979637	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs2279501	0.85[CHB][hapmap]
rs2279502	0.90[CHB][hapmap]
rs2337685	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2337686	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2338019	0.85[CHB][hapmap]
rs2338206	0.85[ASN][1000 genomes]
rs28415528	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2932579	0.85[CHB][hapmap]
rs2932580	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932590	0.95[CHB][hapmap]
rs2999526	0.95[CHB][hapmap]
rs2999528	0.95[CHB][hapmap]
rs2999531	0.90[CHB][hapmap]
rs3007708	0.90[CHB][hapmap]
rs34251437	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3791153	0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4845719	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56000812	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56078223	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56170235	0.85[ASN][1000 genomes]
rs56313205	0.86[ASN][1000 genomes]
rs57674198	0.85[ASN][1000 genomes]
rs57785325	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58087484	0.85[ASN][1000 genomes]
rs61814883	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61817695	0.85[ASN][1000 genomes]
rs61817697	0.83[ASN][1000 genomes]
rs61817719	0.88[ASN][1000 genomes]
rs61817720	0.88[ASN][1000 genomes]
rs61817722	0.96[ASN][1000 genomes]
rs61817723	0.94[ASN][1000 genomes]
rs61817724	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61817725	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6587632	0.88[ASN][1000 genomes]
rs6587633	0.88[ASN][1000 genomes]
rs6587634	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6587635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587637	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587640	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6657658	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6659662	0.83[ASN][1000 genomes]
rs6662602	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6662611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6662728	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663064	0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6672064	0.84[ASN][1000 genomes]
rs6675930	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6678672	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6682605	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6684114	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6686874	0.95[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6691212	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6693388	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6693396	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6693901	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6695324	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6701374	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6703448	0.88[ASN][1000 genomes]
rs6703465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72694840	0.86[ASN][1000 genomes]
rs7535002	0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7538652	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7541099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554832	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554859	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs971887	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943221	0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9943251	0.85[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases
6	nsv2855	chr1:151936470-151966381	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6587638	S100A10	Cis_1M	lymphoblastoid	RTeQTL
rs6587638	S100A10	cis	multi-tissue	Pritchard
rs6587638	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs6587638	NBPF18P	cis	Nerve Tibial	GTEx
rs6587638	THEM4	cis	multi-tissue	Pritchard
rs6587638	THEM4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151930800-151940800	Weak transcription	NHDF-Ad	bronchial
2	chr1:151933600-151945000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:151934000-151940600	Weak transcription	Gastric	stomach
4	chr1:151934200-151940600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:151934200-151942600	Weak transcription	HSMM	muscle
6	chr1:151934400-151940200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:151934600-151940600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:151934600-151953400	Weak transcription	Psoas Muscle	Psoas
9	chr1:151934800-151939600	Weak transcription	Fetal Intestine Small	intestine
10	chr1:151934800-151940200	Weak transcription	Fetal Intestine Large	intestine
11	chr1:151935200-151940400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:151936000-151945000	Weak transcription	HSMMtube	muscle
13	chr1:151936400-151938800	Weak transcription	Hela-S3	cervix
14	chr1:151937200-151938800	Weak transcription	HUVEC	blood vessel
15	chr1:151937200-151940200	Weak transcription	Adipose Nuclei	Adipose
16	chr1:151937200-151940200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:151937200-151940400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:151937200-151940400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:151937200-151940600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:151937200-151940600	Weak transcription	Left Ventricle	heart
21	chr1:151937200-151940600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:151937200-151940800	Weak transcription	Spleen	Spleen
23	chr1:151937200-151945000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:151937400-151938400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:151937400-151938400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:151937400-151938400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:151937400-151939800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:151937400-151940200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:151937400-151940200	Weak transcription	Stomach Mucosa	stomach
30	chr1:151937400-151940400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:151937400-151940600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:151937400-151940600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:151937400-151940600	Weak transcription	Lung	lung
34	chr1:151937800-151938200	Weak transcription	NHEK	skin

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