Variant report

Variant	rs6974485
Chromosome Location	chr7:66614306-66614307
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10215275	0.82[EUR][1000 genomes]
rs10228308	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap]
rs10228489	0.88[AFR][1000 genomes]
rs10228714	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10233388	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10233967	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10234493	0.80[AFR][1000 genomes]
rs10234659	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs10235308	0.82[EUR][1000 genomes]
rs10238245	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap]
rs10242790	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap]
rs10248168	0.81[EUR][1000 genomes]
rs10250751	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10262781	0.83[EUR][1000 genomes]
rs10268701	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10269534	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10271374	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10273692	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10274165	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10274305	0.82[EUR][1000 genomes]
rs10274725	0.82[AFR][1000 genomes]
rs11763486	0.82[EUR][1000 genomes]
rs11765481	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11769413	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11769745	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11770086	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11771105	0.81[AFR][1000 genomes]
rs11771227	0.81[EUR][1000 genomes]
rs11773012	0.82[EUR][1000 genomes]
rs11773691	0.82[EUR][1000 genomes]
rs13222146	0.95[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs13222233	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13222367	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13225639	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13229085	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs14318	0.83[AFR][1000 genomes]
rs17137288	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap]
rs17144722	0.86[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap]
rs17180957	0.90[JPT][hapmap]
rs1829931	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1880278	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2421404	1.00[CHB][hapmap]
rs2690147	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs28373802	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2844097	0.91[CEU][hapmap]
rs2844170	0.82[AFR][1000 genomes]
rs28465142	0.86[EUR][1000 genomes]
rs28620117	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs28813778	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs28888421	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2901425	0.84[EUR][1000 genomes]
rs2960982	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34762791	0.83[EUR][1000 genomes]
rs35122750	0.84[EUR][1000 genomes]
rs35408354	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35470341	0.84[EUR][1000 genomes]
rs3857691	0.84[EUR][1000 genomes]
rs4083135	0.83[EUR][1000 genomes]
rs4382353	0.80[EUR][1000 genomes]
rs4593419	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4718475	0.89[CEU][hapmap];0.82[CHB][hapmap]
rs55829112	0.82[EUR][1000 genomes]
rs62464963	0.82[AFR][1000 genomes]
rs6460322	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6460325	0.82[EUR][1000 genomes]
rs6460326	0.82[EUR][1000 genomes]
rs6460327	0.82[EUR][1000 genomes]
rs6460328	0.82[EUR][1000 genomes]
rs6460329	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6460330	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66744554	0.81[EUR][1000 genomes]
rs66908665	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6948003	0.80[AFR][1000 genomes]
rs6948008	0.82[AFR][1000 genomes]
rs6949104	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6950170	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap]
rs6950847	0.81[EUR][1000 genomes]
rs6951192	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6952309	0.84[EUR][1000 genomes]
rs6958165	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6958481	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6966142	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6978418	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6978918	0.86[EUR][1000 genomes]
rs71523750	0.80[EUR][1000 genomes]
rs71563168	0.82[EUR][1000 genomes]
rs7350000	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7350002	0.82[EUR][1000 genomes]
rs7350057	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7779596	0.83[EUR][1000 genomes]
rs7780458	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap]
rs7783513	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7783776	0.81[AFR][1000 genomes]
rs7783888	0.90[AFR][1000 genomes]
rs7791853	0.85[TSI][hapmap]
rs7792212	0.82[EUR][1000 genomes]
rs7793101	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7793104	0.81[EUR][1000 genomes]
rs7794060	0.80[AFR][1000 genomes]
rs7794130	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7796133	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7797608	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7811122	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7811268	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9690120	0.84[EUR][1000 genomes]
rs9690121	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9690145	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9690291	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9690839	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9692120	0.82[AFR][1000 genomes]
rs9692192	0.82[EUR][1000 genomes]
rs9692303	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv888330	chr7:66502171-66877880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv831019	chr7:66516808-66720485	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv966838	chr7:66548076-66617503	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
6	esv1802655	chr7:66576034-66634666	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	esv1816643	chr7:66576034-66634666	Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
8	esv1840497	chr7:66576034-66634666	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	esv1851064	chr7:66576034-66634666	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
10	esv1850306	chr7:66601324-66632583	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
11	esv1832033	chr7:66601324-66637001	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
12	esv1822512	chr7:66613751-66637001	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases
13	esv1826252	chr7:66613751-66637001	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6974485	STAG3L4	cis	Nerve Tibial	GTEx
rs6974485	TYW1	cis	normal skin	skin_eQTL
rs6974485	ERV3	cis	parietal	SCAN
rs6974485	ZNF117	cis	parietal	SCAN
rs6974485	TYW1	cis	Brain Pons	GTEx
rs6974485	ZNF117	cis	cerebellum	SCAN
rs6974485	ASL	cis	cerebellum	SCAN
rs6974485	TYW1	cis	lymphoblastoid	seeQTL
rs6974485	TYW1	cis	Esophagus Mucosa	GTEx
rs6974485	TYW1	cis	Muscle Skeletal	GTEx
rs6974485	FLJ13195	cis	multi-tissue	Pritchard
rs6974485	TYW1	cis	Heart Left Ventricle	GTEx
rs6974485	TYW1	cis	Nerve Tibial	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66533800-66623200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr7:66545600-66616600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:66550000-66624000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:66576600-66616600	Weak transcription	Fetal Stomach	stomach
5	chr7:66584400-66624400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr7:66585000-66622400	Weak transcription	HSMM	muscle
7	chr7:66585000-66623600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr7:66585200-66627200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:66591400-66620000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:66591600-66626400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:66594000-66622000	Weak transcription	Pancreas	Pancrea
12	chr7:66594200-66623800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr7:66594600-66614800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr7:66594600-66615800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr7:66594600-66617800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr7:66594600-66620200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr7:66594600-66621800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr7:66594800-66623000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr7:66594800-66626800	Weak transcription	Dnd41	blood
20	chr7:66595000-66618800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr7:66595000-66627400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr7:66595200-66616400	Weak transcription	GM12878-XiMat	blood
23	chr7:66595400-66620400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr7:66595600-66616600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr7:66596000-66618800	Weak transcription	Fetal Intestine Large	intestine
26	chr7:66596000-66619200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr7:66596000-66620200	Weak transcription	Primary B cells from cord blood	blood
28	chr7:66596000-66620400	Weak transcription	Adipose Nuclei	Adipose
29	chr7:66598600-66616400	Weak transcription	Fetal Intestine Small	intestine
30	chr7:66600400-66623400	Weak transcription	Brain Hippocampus Middle	brain
31	chr7:66600800-66625000	Weak transcription	Left Ventricle	heart
32	chr7:66603200-66617000	Weak transcription	Primary T cells from cord blood	blood
33	chr7:66603200-66626600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr7:66604600-66624000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr7:66608800-66614800	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr7:66608800-66628200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:66608800-66632600	Weak transcription	Ovary	ovary
38	chr7:66609800-66620400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr7:66609800-66624400	Weak transcription	Liver	Liver
40	chr7:66612000-66619600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr7:66612000-66620200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr7:66612400-66627600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr7:66613200-66626400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:66614000-66614400	Enhancers	Fetal Heart	heart
45	chr7:66614200-66614400	Enhancers	Primary hematopoietic stem cells	blood
46	chr7:66614200-66628000	Weak transcription	K562	blood

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