Variant report

Variant	rs6973457
Chromosome Location	chr7:120656628-120656629
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10229719	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10258025	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11363	0.86[EUR][1000 genomes]
rs12672149	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13881	1.00[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs193727	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2013083	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013087	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074576	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2074577	0.85[CEU][hapmap]
rs2215786	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215789	0.92[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2244863	0.84[CEU][hapmap]
rs2244865	0.85[CEU][hapmap]
rs2525711	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525712	0.85[CEU][hapmap]
rs2525713	0.85[CEU][hapmap]
rs2525714	1.00[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs2525715	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2525716	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525717	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525718	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525719	0.89[CEU][hapmap]
rs2525720	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525722	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525723	0.85[EUR][1000 genomes]
rs2525724	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525725	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs2525726	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2525728	1.00[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs2525731	0.90[EUR][1000 genomes]
rs2525732	0.88[EUR][1000 genomes]
rs2525733	1.00[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs2525734	1.00[CEU][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs2525735	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2525738	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2525739	1.00[CEU][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2525740	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2721350	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2721351	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2721359	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2721361	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2721366	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2721368	1.00[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs2721370	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs2721372	0.89[CEU][hapmap]
rs2896299	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3944026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41688	0.85[CEU][hapmap]
rs41691	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41692	1.00[CEU][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41693	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41694	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41695	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41697	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41698	0.93[ASN][1000 genomes]
rs41703	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs41704	1.00[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4727915	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730985	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730987	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953795	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6966297	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7789501	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808535	0.92[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	nsv831114	chr7:120595624-120804510	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv608327	chr7:120633006-120873078	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv2753621	chr7:120635049-120800049	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1030988	chr7:120636796-120672504	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1023611	chr7:120638930-120881658	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6973457	SPAM1	cis	parietal	SCAN
rs6973457	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120637200-120663600	Weak transcription	Right Ventricle	heart
2	chr7:120647200-120657000	Weak transcription	Fetal Kidney	kidney
3	chr7:120647200-120658800	Weak transcription	Fetal Muscle Leg	muscle
4	chr7:120647800-120657800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr7:120649400-120663600	Weak transcription	Left Ventricle	heart
6	chr7:120652600-120660600	Genic enhancers	K562	blood
7	chr7:120652800-120663800	Weak transcription	Small Intestine	intestine
8	chr7:120653200-120657600	Weak transcription	Fetal Lung	lung
9	chr7:120653400-120656800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:120653400-120663600	Weak transcription	Psoas Muscle	Psoas
11	chr7:120654600-120659600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr7:120654800-120658000	Enhancers	Stomach Smooth Muscle	stomach
13	chr7:120654800-120663600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr7:120655000-120658000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr7:120655000-120660200	Enhancers	Colon Smooth Muscle	Colon
16	chr7:120655400-120657000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:120655600-120657000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr7:120655600-120657000	Weak transcription	Aorta	Aorta
19	chr7:120655800-120657000	Strong transcription	Adipose Nuclei	Adipose
20	chr7:120655800-120657400	Strong transcription	Liver	Liver
21	chr7:120655800-120659000	Weak transcription	Fetal Heart	heart
22	chr7:120656000-120663600	Weak transcription	Ovary	ovary
23	chr7:120656000-120668000	Weak transcription	Right Atrium	heart
24	chr7:120656200-120657200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr7:120656200-120660000	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr7:120656400-120657000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
27	chr7:120656400-120657000	Strong transcription	HSMMtube	muscle
28	chr7:120656400-120657200	Genic enhancers	NHDF-Ad	bronchial
29	chr7:120656400-120658000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:120656400-120658000	Enhancers	Fetal Stomach	stomach
31	chr7:120656400-120659000	Genic enhancers	NHLF	lung
32	chr7:120656400-120661800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr7:120656400-120661800	Enhancers	Osteobl	bone
34	chr7:120656600-120656800	Genic enhancers	Muscle Satellite Cultured Cells	--
35	chr7:120656600-120657800	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr7:120656600-120659200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr7:120656600-120659600	Enhancers	Rectal Smooth Muscle	rectum
38	chr7:120656600-120661000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr7:120656600-120661400	Genic enhancers	HSMM	muscle

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