Variant report

Variant	rs4038586
Chromosome Location	chr3:136363291-136363292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136360867..136363380-chr3:136456006..136458080,2	MCF-7	breast:
2	chr3:136362757..136364544-chr3:136367826..136369357,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240695	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1052620	1.00[ASN][1000 genomes]
rs12695649	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062352	1.00[ASN][1000 genomes]
rs13066401	1.00[ASN][1000 genomes]
rs13071220	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080786	1.00[ASN][1000 genomes]
rs13092193	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096466	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100192	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13314357	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13316214	1.00[ASN][1000 genomes]
rs13321721	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13326151	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13433683	1.00[ASN][1000 genomes]
rs13433688	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434116	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604793	1.00[ASN][1000 genomes]
rs17298525	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17364492	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17365792	1.00[ASN][1000 genomes]
rs1872239	1.00[ASN][1000 genomes]
rs2176269	1.00[ASN][1000 genomes]
rs28390205	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28472992	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28634226	1.00[ASN][1000 genomes]
rs28641809	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28718456	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28750366	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28811905	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28877020	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34135127	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34168675	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34282798	1.00[ASN][1000 genomes]
rs34564818	1.00[ASN][1000 genomes]
rs34645606	1.00[ASN][1000 genomes]
rs34757183	1.00[ASN][1000 genomes]
rs34804893	0.84[ASW][hapmap];0.93[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34913797	1.00[ASN][1000 genomes]
rs34969907	1.00[ASN][1000 genomes]
rs35096613	1.00[ASN][1000 genomes]
rs35100027	1.00[ASN][1000 genomes]
rs35198484	1.00[ASN][1000 genomes]
rs35210994	1.00[ASN][1000 genomes]
rs35326900	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35422852	1.00[ASN][1000 genomes]
rs35428413	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35880395	1.00[ASN][1000 genomes]
rs35899944	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs36109616	1.00[ASN][1000 genomes]
rs66509730	1.00[ASN][1000 genomes]
rs66890203	1.00[ASN][1000 genomes]
rs67145204	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67382287	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768743	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6771002	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773949	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774964	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775314	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6775466	0.85[LWK][hapmap]
rs67949818	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6806123	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71336069	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71336080	1.00[ASN][1000 genomes]
rs73230043	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230099	1.00[ASN][1000 genomes]
rs73231903	1.00[ASN][1000 genomes]
rs7612425	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9289513	0.84[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs9809269	1.00[ASN][1000 genomes]
rs9809988	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs9810789	1.00[ASN][1000 genomes]
rs9812579	1.00[ASN][1000 genomes]
rs9813376	1.00[ASN][1000 genomes]
rs9813691	1.00[CEU][hapmap];0.82[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9818056	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9819856	1.00[ASN][1000 genomes]
rs9820717	0.84[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823373	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9828088	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828976	1.00[ASN][1000 genomes]
rs9838884	0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs9839137	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9841529	1.00[ASN][1000 genomes]
rs9845862	0.84[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs9847427	0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850364	1.00[ASN][1000 genomes]
rs9857833	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857966	1.00[CEU][hapmap];0.82[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858560	1.00[ASN][1000 genomes]
rs9860879	1.00[ASN][1000 genomes]
rs9865995	1.00[ASN][1000 genomes]
rs9867325	1.00[ASN][1000 genomes]
rs9869630	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871184	1.00[ASN][1000 genomes]
rs9873536	1.00[ASN][1000 genomes]
rs9875770	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878078	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881831	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883189	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4038586	GRK7	cis	cerebellum	SCAN
rs4038586	ERICH1	trans	parietal	SCAN
rs4038586	PPP2R3A	cis	cerebellum	SCAN
rs4038586	PPP2R3A	cis	parietal	SCAN
rs4038586	ZBTB38	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136316000-136364400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr3:136324200-136363600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:136336200-136364800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:136345800-136364000	Weak transcription	Small Intestine	intestine
5	chr3:136347200-136368400	Weak transcription	Fetal Intestine Small	intestine
6	chr3:136347400-136364000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:136347600-136367200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:136348200-136365000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr3:136348600-136364600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:136348800-136363800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:136348800-136373600	Weak transcription	Thymus	Thymus
12	chr3:136349800-136372400	Weak transcription	Dnd41	blood
13	chr3:136350600-136372200	Weak transcription	Primary T cells from cord blood	blood
14	chr3:136351600-136364600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr3:136351600-136364800	Weak transcription	Pancreas	Pancrea
16	chr3:136351600-136376200	Weak transcription	Esophagus	oesophagus
17	chr3:136351800-136364000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:136351800-136364600	Weak transcription	Right Ventricle	heart
19	chr3:136352000-136364000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:136352400-136371600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:136352400-136371600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:136352400-136371800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:136354400-136364000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:136356000-136364600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:136356600-136364000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:136357800-136368200	Weak transcription	Lung	lung
27	chr3:136357800-136387400	Weak transcription	Fetal Thymus	thymus
28	chr3:136358200-136363600	Weak transcription	Ovary	ovary
29	chr3:136358200-136363600	Weak transcription	Psoas Muscle	Psoas
30	chr3:136361400-136366200	Weak transcription	Fetal Stomach	stomach
31	chr3:136361800-136364600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:136362000-136364800	Weak transcription	K562	blood
33	chr3:136363200-136363400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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