Variant report

Variant	rs949678
Chromosome Location	chr6:45912981-45912982
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	chr6:45903397..45906040-chr6:45911474..45913451,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112782	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12055836	1.00[CEU][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes]
rs12662995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777566	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs3777569	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs3777570	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs3777574	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777575	1.00[CEU][hapmap];0.95[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];0.97[ASN][1000 genomes]
rs3777576	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777577	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777578	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777587	0.94[AFR][1000 genomes]
rs3777589	0.86[ASW][hapmap];0.88[AFR][1000 genomes]
rs3798263	1.00[CEU][hapmap]
rs3798266	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3822886	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3822887	0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6907979	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9357496	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9395137	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs946226	1.00[CEU][hapmap];1.00[MEX][hapmap];0.89[AMR][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	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv517891	chr6:45899823-45915088	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45898600-45914600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:45898600-45916800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:45898800-45919200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr6:45903000-45917200	Strong transcription	Fetal Intestine Large	intestine
5	chr6:45903400-45914400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr6:45907000-45916600	Weak transcription	Pancreas	Pancrea
7	chr6:45907400-45917600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:45907800-45916400	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr6:45908000-45918600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr6:45908200-45918200	Weak transcription	Colonic Mucosa	Colon
11	chr6:45908800-45913800	Weak transcription	Ovary	ovary
12	chr6:45908800-45914600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:45909000-45913200	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:45910600-45915400	Enhancers	Fetal Heart	heart
15	chr6:45910800-45913800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:45911000-45919200	Weak transcription	Small Intestine	intestine
17	chr6:45911000-45923600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr6:45911200-45913400	Weak transcription	Fetal Intestine Small	intestine
19	chr6:45911200-45913800	Weak transcription	Placenta	Placenta
20	chr6:45911200-45918000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:45911400-45919000	Weak transcription	Adipose Nuclei	Adipose
22	chr6:45911600-45913800	Weak transcription	Right Atrium	heart
23	chr6:45911600-45914200	Weak transcription	Lung	lung
24	chr6:45911600-45914200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr6:45911800-45914600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr6:45912400-45913000	Enhancers	Fetal Lung	lung
27	chr6:45912400-45914600	Enhancers	Psoas Muscle	Psoas
28	chr6:45912400-45917200	Genic enhancers	Left Ventricle	heart
29	chr6:45912600-45915400	Genic enhancers	Right Ventricle	heart
30	chr6:45912600-45916600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:45912600-45923000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
32	chr6:45912800-45913800	Weak transcription	Fetal Kidney	kidney
33	chr6:45912800-45928400	Weak transcription	Spleen	Spleen

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