Variant report

Variant	rs2517511
Chromosome Location	chr6:31029918-31029919
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:31010707..31012864-chr6:31028593..31030504,2	MCF-7	breast:
2	chr6:31020716..31023487-chr6:31028398..31030708,2	K562	blood:
3	chr6:30580660..30582853-chr6:31029562..31031362,2	K562	blood:

Variant related genes	Relation type
ENSG00000228789	Chromatin interaction

Extended variants
information (count: 168 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs1064190	0.80[ASN][1000 genomes]
rs1064191	0.80[ASN][1000 genomes]
rs1265054	0.80[ASN][1000 genomes]
rs1265055	0.80[ASN][1000 genomes]
rs1265056	0.80[ASN][1000 genomes]
rs1265058	0.80[ASN][1000 genomes]
rs1265059	0.80[ASN][1000 genomes]
rs1265063	0.80[ASN][1000 genomes]
rs1265064	0.80[ASN][1000 genomes]
rs2106067	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2246330	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2249231	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2249485	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2249486	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2249876	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2251825	0.85[ASN][1000 genomes]
rs2252195	0.85[ASN][1000 genomes]
rs2256436	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2394420	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2394424	0.85[ASN][1000 genomes]
rs2428520	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2429721	0.82[ASN][1000 genomes]
rs2517414	0.83[ASN][1000 genomes]
rs2517423	0.83[ASN][1000 genomes]
rs2517427	0.83[ASN][1000 genomes]
rs2517440	0.83[ASN][1000 genomes]
rs2517450	0.83[ASN][1000 genomes]
rs2517452	0.83[ASN][1000 genomes]
rs2517453	0.83[ASN][1000 genomes]
rs2517455	0.83[ASN][1000 genomes]
rs2517458	0.83[ASN][1000 genomes]
rs2517460	0.83[ASN][1000 genomes]
rs2517464	0.82[ASN][1000 genomes]
rs2517465	0.83[ASN][1000 genomes]
rs2517470	0.81[ASN][1000 genomes]
rs2517471	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2517472	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2517475	0.81[ASN][1000 genomes]
rs2517476	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2517477	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2517478	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2517480	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2517483	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2517488	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2517489	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2517492	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2517493	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2517497	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2517500	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517501	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2517502	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517504	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517507	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517510	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517513	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517516	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517520	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2517523	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517524	0.81[AMR][1000 genomes]
rs2517525	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517532	0.85[ASN][1000 genomes]
rs2517533	0.85[ASN][1000 genomes]
rs2517534	0.81[ASN][1000 genomes]
rs2517541	0.81[ASN][1000 genomes]
rs2517556	0.81[ASN][1000 genomes]
rs2523836	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2523837	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2523838	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2523843	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2523846	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2523852	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2523854	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2523856	0.81[ASN][1000 genomes]
rs2523858	0.85[ASN][1000 genomes]
rs2523860	0.85[ASN][1000 genomes]
rs2523862	0.85[ASN][1000 genomes]
rs2523878	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2523880	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523881	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523883	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2523884	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523885	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523886	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523888	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523889	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523890	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2523891	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523893	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523894	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2523895	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2523896	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2535277	0.80[ASN][1000 genomes]
rs2535282	0.83[ASN][1000 genomes]
rs2535283	0.83[ASN][1000 genomes]
rs2535287	0.83[ASN][1000 genomes]
rs2535288	0.82[ASN][1000 genomes]
rs2535289	0.83[ASN][1000 genomes]
rs2535290	0.83[ASN][1000 genomes]
rs2535291	0.83[ASN][1000 genomes]
rs2535292	0.83[ASN][1000 genomes]
rs2535293	0.83[ASN][1000 genomes]
rs2535297	0.83[ASN][1000 genomes]
rs2535299	0.83[ASN][1000 genomes]
rs2535301	0.83[ASN][1000 genomes]
rs2535302	0.81[ASN][1000 genomes]
rs2535303	0.85[ASN][1000 genomes]
rs2535304	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2535305	0.85[ASN][1000 genomes]
rs2535306	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2535307	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2535308	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2535309	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2535310	0.85[ASN][1000 genomes]
rs2535311	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2535312	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2535313	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2535314	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2535315	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2844641	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2905757	0.86[ASN][1000 genomes]
rs2905759	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3095305	0.83[ASN][1000 genomes]
rs3130546	0.83[ASN][1000 genomes]
rs3130957	0.82[ASN][1000 genomes]
rs3130960	0.81[ASN][1000 genomes]
rs3130961	0.83[ASN][1000 genomes]
rs3130962	0.81[ASN][1000 genomes]
rs3130963	0.83[ASN][1000 genomes]
rs3130964	0.83[ASN][1000 genomes]
rs3130970	0.83[ASN][1000 genomes]
rs3131789	0.83[ASN][1000 genomes]
rs3131796	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3915966	0.85[ASN][1000 genomes]
rs6921557	0.81[ASN][1000 genomes]
rs6940894	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6941772	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7381897	0.80[ASN][1000 genomes]
rs7755184	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9262625	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9262628	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9262629	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9262697	0.84[AMR][1000 genomes]
rs9263456	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9263464	0.82[AMR][1000 genomes]
rs9263465	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9263466	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9263473	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9263474	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9263493	0.83[ASN][1000 genomes]
rs9263494	0.83[ASN][1000 genomes]
rs9263593	0.81[ASN][1000 genomes]
rs9263597	0.81[ASN][1000 genomes]
rs9263631	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv884130	chr6:31014305-31038756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv884131	chr6:31014305-31040725	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv884132	chr6:31014305-31057183	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv884133	chr6:31024673-31036148	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
12	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
13	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
14	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
15	nsv884134	chr6:31028345-31048263	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2517511	ZNF187	cis	cerebellum	SCAN
rs2517511	HCG22	cis	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31022200-31050800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:31026000-31030200	Weak transcription	Esophagus	oesophagus
3	chr6:31026000-31034800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:31026200-31036200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:31026200-31038000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:31027200-31032600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:31027200-31032800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:31027400-31030600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr6:31027400-31033400	Weak transcription	Brain Angular Gyrus	brain
10	chr6:31027600-31033400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:31027600-31033600	Weak transcription	Brain Substantia Nigra	brain
12	chr6:31028200-31033600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr6:31028200-31036200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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