Variant report

Variant	rs6949083
Chromosome Location	chr7:65889746-65889747
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXP2	chr7:65889729-65889966	PFSK-1	brain:	n/a	n/a

Variant related genes	Relation type
SKP1P1	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10081172	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10226294	0.86[EUR][1000 genomes]
rs10228381	0.87[EUR][1000 genomes]
rs10236665	0.96[EUR][1000 genomes]
rs10239200	0.85[EUR][1000 genomes]
rs10244602	0.86[EUR][1000 genomes]
rs10247852	0.91[EUR][1000 genomes]
rs10255813	0.86[EUR][1000 genomes]
rs10264619	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10266041	0.84[EUR][1000 genomes]
rs10275413	0.96[EUR][1000 genomes]
rs10277231	0.82[EUR][1000 genomes]
rs10278763	0.87[EUR][1000 genomes]
rs10280717	0.85[EUR][1000 genomes]
rs10281544	0.84[EUR][1000 genomes]
rs12333749	0.83[EUR][1000 genomes]
rs16868546	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1862086	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1895134	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2420598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28455065	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28474923	0.86[EUR][1000 genomes]
rs28526115	0.87[EUR][1000 genomes]
rs28606020	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28657758	0.87[EUR][1000 genomes]
rs3757417	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3764904	0.84[EUR][1000 genomes]
rs4149463	0.81[ASN][1000 genomes]
rs4518552	0.84[EUR][1000 genomes]
rs4587218	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57902746	0.84[EUR][1000 genomes]
rs58123804	0.98[EUR][1000 genomes]
rs58973756	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60344524	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61132090	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73133809	0.85[EUR][1000 genomes]
rs73133816	0.86[EUR][1000 genomes]
rs73144219	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73148698	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73152708	0.86[EUR][1000 genomes]
rs73152719	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73152725	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised 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	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised 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	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers 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	69 gene(s)	inside rSNPs	diseases
5	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers 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 miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv482441	chr7:65885824-66061788	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv1802195	chr7:65886451-65945211	Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv970514	chr7:65887884-65891263	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6949083	GS1-124K5.12	cis	Skin Sun Exposed Lower leg	GTEx
rs6949083	GS1-124K5.12	cis	Adipose Subcutaneous	GTEx
rs6949083	GS1-124K5.12	cis	lung	GTEx
rs6949083	GS1-124K5.12	cis	Artery Tibial	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65879000-65890000	Weak transcription	HSMM	muscle
2	chr7:65879000-65891800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:65879000-65893200	Weak transcription	Aorta	Aorta
4	chr7:65879000-65905600	Weak transcription	Lung	lung
5	chr7:65879000-65909000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:65879000-65922200	Weak transcription	Small Intestine	intestine
7	chr7:65879200-65891400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr7:65879200-65893000	Weak transcription	Gastric	stomach
9	chr7:65879200-65893800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:65879200-65894600	Weak transcription	HMEC	breast
11	chr7:65879200-65894800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr7:65879200-65896000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr7:65879200-65902000	Weak transcription	Brain Substantia Nigra	brain
14	chr7:65879200-65904000	Weak transcription	Fetal Lung	lung
15	chr7:65879200-65907400	Weak transcription	Esophagus	oesophagus
16	chr7:65879200-65924600	Weak transcription	Brain Anterior Caudate	brain
17	chr7:65879200-65939800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr7:65879200-65946000	Weak transcription	NHEK	skin
19	chr7:65879200-65957600	Weak transcription	Psoas Muscle	Psoas
20	chr7:65879400-65889800	Weak transcription	Ovary	ovary
21	chr7:65879400-65890800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr7:65879400-65891200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr7:65879400-65891400	Weak transcription	Colonic Mucosa	Colon
24	chr7:65879400-65892600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:65879400-65900600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr7:65879400-65901000	Weak transcription	Brain Angular Gyrus	brain
27	chr7:65879400-65901200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr7:65879400-65909200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr7:65879400-65914200	Weak transcription	Left Ventricle	heart
30	chr7:65879400-65914200	Weak transcription	GM12878-XiMat	blood
31	chr7:65879400-65917200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr7:65879400-65921000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr7:65879400-65921400	Weak transcription	Fetal Kidney	kidney
34	chr7:65879600-65892200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr7:65879600-65893800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr7:65879600-65895000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr7:65879600-65899400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr7:65879600-65900600	Weak transcription	Brain Germinal Matrix	brain
39	chr7:65879600-65907600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr7:65879600-65913600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr7:65879600-65919000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr7:65879600-65920400	Weak transcription	Primary B cells from cord blood	blood
43	chr7:65879800-65889800	Weak transcription	Fetal Thymus	thymus
44	chr7:65879800-65891200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr7:65879800-65893000	Weak transcription	Pancreas	Pancrea
46	chr7:65879800-65893600	Weak transcription	Spleen	Spleen
47	chr7:65879800-65913600	Weak transcription	Fetal Muscle Trunk	muscle
48	chr7:65881000-65895000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr7:65881200-65894600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr7:65881200-65894600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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