Variant report

Variant	rs11964846
Chromosome Location	chr6:15490551-15490552
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15474184..15476635-chr6:15488076..15490844,2	K562	blood:
2	chr6:15483229..15486068-chr6:15489614..15491902,2	MCF-7	breast:
3	chr6:15489579..15491671-chr6:15507006..15508555,2	MCF-7	breast:
4	chr6:15243868..15248249-chr6:15486712..15491085,4	K562	blood:
5	chr6:15480753..15482538-chr6:15489895..15492218,2	K562	blood:
6	chr6:15478158..15480159-chr6:15489862..15492490,2	K562	blood:

Variant related genes	Relation type
ENSG00000271888	Chromatin interaction
ENSG00000008083	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10949304	0.90[ASN][1000 genomes]
rs11966626	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13192234	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13192892	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13194650	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13196869	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13198780	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13202100	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13202955	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13204842	1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13208563	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13209668	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17455404	1.00[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs1967664	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2076056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237138	0.87[EUR][1000 genomes]
rs2299043	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs35868206	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3819396	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4712251	0.92[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4715975	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4715979	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4715980	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6899342	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6899343	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6917591	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs742099	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs742100	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756331	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7761778	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7769291	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7774429	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9383056	0.86[EUR][1000 genomes]
rs9383062	0.93[EUR][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	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15461600-15491000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:15471000-15502000	Weak transcription	A549	lung
3	chr6:15480400-15490600	Weak transcription	NHDF-Ad	bronchial
4	chr6:15481200-15491800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:15482200-15491400	Weak transcription	Fetal Brain Male	brain
6	chr6:15482400-15491400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:15483200-15490800	Weak transcription	HSMMtube	muscle
8	chr6:15483200-15491400	Weak transcription	Fetal Heart	heart
9	chr6:15484800-15496400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:15486200-15491000	Strong transcription	Primary B cells from cord blood	blood
11	chr6:15486200-15491400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:15486400-15491600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:15486600-15491400	Weak transcription	Right Atrium	heart
14	chr6:15486800-15490800	Weak transcription	Psoas Muscle	Psoas
15	chr6:15486800-15502000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr6:15487000-15490600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:15487000-15490800	Strong transcription	Fetal Stomach	stomach
18	chr6:15487200-15491000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr6:15487200-15508000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr6:15487400-15490800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:15487600-15490600	Strong transcription	Fetal Muscle Leg	muscle
22	chr6:15487600-15491000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:15488600-15491000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr6:15488800-15491800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
25	chr6:15488800-15493000	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr6:15489000-15491400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr6:15489000-15491600	Weak transcription	Brain Germinal Matrix	brain
28	chr6:15489000-15492600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr6:15489200-15490800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:15489200-15491400	Weak transcription	Stomach Mucosa	stomach
31	chr6:15489200-15495800	Weak transcription	HMEC	breast
32	chr6:15489200-15496200	Weak transcription	Small Intestine	intestine
33	chr6:15489200-15496800	Weak transcription	Colonic Mucosa	Colon
34	chr6:15489200-15504400	Weak transcription	Fetal Brain Female	brain
35	chr6:15489400-15491400	Weak transcription	NH-A	brain
36	chr6:15489400-15491600	Weak transcription	Placenta	Placenta
37	chr6:15489400-15491800	Weak transcription	HSMM	muscle
38	chr6:15489400-15493000	Genic enhancers	Fetal Thymus	thymus
39	chr6:15489400-15493200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:15489600-15491400	Genic enhancers	Primary hematopoietic stem cells	blood
41	chr6:15489600-15491400	Weak transcription	Osteobl	bone
42	chr6:15489600-15492800	Genic enhancers	Thymus	Thymus
43	chr6:15489600-15493400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:15489600-15495400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:15489800-15490800	Weak transcription	Colon Smooth Muscle	Colon
46	chr6:15489800-15490800	Weak transcription	Fetal Kidney	kidney
47	chr6:15489800-15491000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:15489800-15491200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:15489800-15491200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr6:15489800-15491400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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