Variant report

Variant	rs7646723
Chromosome Location	chr3:136364511-136364512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136362757..136364544-chr3:136367826..136369357,2	MCF-7	breast:
2	chr3:136364480..136366014-chr3:136376930..136379520,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10513016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843991	1.00[CHB][hapmap]
rs16844056	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17365351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17466223	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35375192	1.00[CHB][hapmap]
rs35644083	1.00[CHB][hapmap]
rs3931416	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs4336059	1.00[CHB][hapmap]
rs55763637	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56888009	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57466072	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57681357	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58636237	0.86[EUR][1000 genomes]
rs59361983	0.89[EUR][1000 genomes]
rs59616231	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59696368	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60014495	0.82[EUR][1000 genomes]
rs6439642	1.00[CHB][hapmap]
rs66470158	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66471262	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66637228	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66739346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66902780	0.93[EUR][1000 genomes]
rs67082054	0.81[EUR][1000 genomes]
rs67231188	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67236827	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67281610	0.85[EUR][1000 genomes]
rs67303976	0.85[EUR][1000 genomes]
rs67546863	0.89[EUR][1000 genomes]
rs67621498	0.82[EUR][1000 genomes]
rs6765239	1.00[CHB][hapmap]
rs67663578	0.82[EUR][1000 genomes]
rs6773054	0.83[MKK][hapmap]
rs6773495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs6773604	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs67794070	0.82[EUR][1000 genomes]
rs67888773	0.93[EUR][1000 genomes]
rs67902591	0.86[EUR][1000 genomes]
rs67923745	0.89[EUR][1000 genomes]
rs6800969	1.00[CHB][hapmap]
rs68018658	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72975363	0.99[EUR][1000 genomes]
rs73228025	0.90[EUR][1000 genomes]
rs73228037	0.93[EUR][1000 genomes]
rs73228040	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230052	0.90[EUR][1000 genomes]
rs73230077	0.83[EUR][1000 genomes]
rs73230078	0.83[EUR][1000 genomes]
rs73230095	0.82[EUR][1000 genomes]
rs7623824	1.00[CHB][hapmap]
rs7636806	0.85[EUR][1000 genomes]
rs7644471	1.00[CHB][hapmap]
rs7646127	0.83[MKK][hapmap]
rs7646563	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820513	1.00[CHB][hapmap]
rs9869957	1.00[CHB][hapmap]
rs9942116	0.81[LWK][hapmap];0.82[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1008866	chr3:136364511-136427790	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv877529	chr3:136364511-136487559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7646723	TMEM22	cis	cerebellum	SCAN
rs7646723	STAG1	cis	cerebellum	SCAN
rs7646723	ATP1B3	cis	cerebellum	SCAN
rs7646723	VCAN	trans	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136336200-136364800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr3:136347200-136368400	Weak transcription	Fetal Intestine Small	intestine
3	chr3:136347600-136367200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:136348200-136365000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr3:136348600-136364600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:136348800-136373600	Weak transcription	Thymus	Thymus
7	chr3:136349800-136372400	Weak transcription	Dnd41	blood
8	chr3:136350600-136372200	Weak transcription	Primary T cells from cord blood	blood
9	chr3:136351600-136364600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:136351600-136364800	Weak transcription	Pancreas	Pancrea
11	chr3:136351600-136376200	Weak transcription	Esophagus	oesophagus
12	chr3:136351800-136364600	Weak transcription	Right Ventricle	heart
13	chr3:136352400-136371600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:136352400-136371600	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr3:136352400-136371800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:136356000-136364600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:136357800-136368200	Weak transcription	Lung	lung
18	chr3:136357800-136387400	Weak transcription	Fetal Thymus	thymus
19	chr3:136361400-136366200	Weak transcription	Fetal Stomach	stomach
20	chr3:136361800-136364600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:136362000-136364800	Weak transcription	K562	blood
22	chr3:136363600-136365000	Enhancers	Ovary	ovary
23	chr3:136363600-136365200	Enhancers	Psoas Muscle	Psoas
24	chr3:136363600-136365400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr3:136364000-136364600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:136364000-136365000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:136364000-136365000	Enhancers	Small Intestine	intestine
28	chr3:136364000-136366200	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr3:136364200-136364600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:136364200-136365200	Flanking Active TSS	GM12878-XiMat	blood
31	chr3:136364200-136368000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr3:136364400-136364800	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr3:136364400-136369400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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