Variant report

Variant	rs2394001
Chromosome Location	chr6:27738699-27738700
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	chr6:27734440..27736801-chr6:27737530..27740059,2	MCF-7	breast:
2	chr6:27738620..27740539-chr6:27758419..27760190,2	MCF-7	breast:

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1010261	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs1015075	0.82[JPT][hapmap]
rs12174918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs169287	0.80[ASN][1000 genomes]
rs175597	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17693877	1.00[CHB][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs183225	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs200466	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs200469	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs200471	0.91[ASN][1000 genomes]
rs200473	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs200478	0.91[ASN][1000 genomes]
rs200479	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs200481	0.98[ASN][1000 genomes]
rs200482	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs200483	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs200484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs200485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs200488	0.93[ASN][1000 genomes]
rs200489	0.93[ASN][1000 genomes]
rs200490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs200497	0.91[ASN][1000 genomes]
rs200498	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs200499	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs200501	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs200948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs200949	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs200950	0.89[ASN][1000 genomes]
rs200952	0.89[ASN][1000 genomes]
rs200953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs200954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs200964	0.80[ASN][1000 genomes]
rs200965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs200966	0.80[ASN][1000 genomes]
rs200968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs200973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs200974	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs200975	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs200976	0.80[ASN][1000 genomes]
rs200977	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs200979	0.82[ASN][1000 genomes]
rs200980	0.82[ASN][1000 genomes]
rs200981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs200983	0.93[ASN][1000 genomes]
rs200989	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs200990	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs200992	0.91[ASN][1000 genomes]
rs200995	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs200996	0.93[ASN][1000 genomes]
rs201002	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2277104	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2747054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs34295134	0.93[ASN][1000 genomes]
rs36108923	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs370155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs390764	0.95[ASN][1000 genomes]
rs401754	0.95[ASN][1000 genomes]
rs401763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4236045	0.82[ASN][1000 genomes]
rs4711158	0.88[AMR][1000 genomes]
rs4711161	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4713116	0.80[AMR][1000 genomes]
rs4713117	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4713122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4713124	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713127	0.86[ASN][1000 genomes]
rs480699	0.84[ASN][1000 genomes]
rs493161	0.86[ASN][1000 genomes]
rs494887	0.82[ASN][1000 genomes]
rs557042	0.86[ASN][1000 genomes]
rs56870390	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56911191	0.81[AMR][1000 genomes]
rs58727692	0.88[AMR][1000 genomes]
rs59015666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666846	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs904142	0.82[JPT][hapmap]
rs9348779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9357041	0.88[AMR][1000 genomes]
rs9357052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9368515	0.88[AMR][1000 genomes]
rs9368516	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[AMR][1000 genomes]
rs9368531	0.95[ASN][1000 genomes]
rs9368534	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9368535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9368536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9368537	0.82[JPT][hapmap]
rs9379987	0.81[AMR][1000 genomes]
rs9379988	0.88[AMR][1000 genomes]
rs9379989	1.00[CEU][hapmap];0.88[AMR][1000 genomes]
rs9379991	0.88[AMR][1000 genomes]
rs9379993	0.80[AMR][1000 genomes]
rs9379997	0.80[AMR][1000 genomes]
rs9380009	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9380013	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9380014	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9380015	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9380018	0.98[ASN][1000 genomes]
rs9380026	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9380028	0.82[JPT][hapmap]
rs9380030	0.82[JPT][hapmap]
rs9393825	0.88[AMR][1000 genomes]
rs9393829	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs9393845	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes]
rs9393854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs9393855	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9393858	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393862	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9468183	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
3	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
4	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
5	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27725600-27743000	Weak transcription	Right Atrium	heart
2	chr6:27730600-27740000	Weak transcription	Spleen	Spleen
3	chr6:27730800-27739000	Weak transcription	Fetal Intestine Small	intestine
4	chr6:27730800-27740000	Weak transcription	Primary T cells from cord blood	blood
5	chr6:27737400-27739000	Weak transcription	K562	blood
6	chr6:27737400-27739600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:27738200-27738800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
8	chr6:27738200-27738800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr6:27738200-27740200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
10	chr6:27738400-27738800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:27738400-27738800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
12	chr6:27738400-27739200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
13	chr6:27738600-27738800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr6:27738600-27739000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:27738600-27739400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:27738600-27739800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:27738600-27739800	Enhancers	Fetal Intestine Large	intestine
18	chr6:27738600-27741600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr6:27738600-27742400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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