Variant report

Variant	rs11967796
Chromosome Location	chr6:56514735-56514736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56499157..56500762-chr6:56514257..56517185,2	MCF-7	breast:
2	chr6:56510440..56512987-chr6:56514462..56516109,2	K562	blood:
3	chr6:56502635..56504912-chr6:56512787..56514887,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL21A1-6	chr6:56514507-56514967	expReg_chr6_5759_-

Extended variants
information (count: 134 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs1024196	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751914	0.94[YRI][hapmap]
rs11961141	0.89[ASN][1000 genomes]
rs11961342	1.00[ASN][1000 genomes]
rs11963288	0.94[EUR][1000 genomes]
rs11966986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968575	1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs11970410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11970648	1.00[CHD][hapmap]
rs13191164	1.00[ASN][1000 genomes]
rs13192478	0.89[ASN][1000 genomes]
rs13192567	0.89[ASN][1000 genomes]
rs13205013	1.00[ASN][1000 genomes]
rs13210876	0.89[ASN][1000 genomes]
rs13213878	0.89[ASN][1000 genomes]
rs13219546	0.89[ASN][1000 genomes]
rs1407831	0.89[EUR][1000 genomes]
rs1535609	0.94[EUR][1000 genomes]
rs1535611	0.94[EUR][1000 genomes]
rs16887928	0.89[EUR][1000 genomes]
rs16888068	1.00[MEX][hapmap]
rs16888070	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16888085	0.90[ASN][1000 genomes]
rs16888096	1.00[ASN][1000 genomes]
rs16888106	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888118	1.00[ASN][1000 genomes]
rs16888124	1.00[ASN][1000 genomes]
rs16888128	1.00[ASN][1000 genomes]
rs16888130	1.00[ASN][1000 genomes]
rs16888133	1.00[ASN][1000 genomes]
rs16888135	0.89[ASN][1000 genomes]
rs16888171	1.00[CHD][hapmap]
rs2144407	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2180148	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207678	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2397224	0.89[EUR][1000 genomes]
rs28633631	1.00[EUR][1000 genomes]
rs2967960	0.89[ASN][1000 genomes]
rs3002003	0.89[ASN][1000 genomes]
rs3002004	0.89[ASN][1000 genomes]
rs34138864	0.90[ASN][1000 genomes]
rs34429594	1.00[ASN][1000 genomes]
rs34724718	1.00[ASN][1000 genomes]
rs34812826	0.89[ASN][1000 genomes]
rs34824960	0.89[ASN][1000 genomes]
rs35089136	0.89[ASN][1000 genomes]
rs35206656	1.00[ASN][1000 genomes]
rs35637749	1.00[ASN][1000 genomes]
rs35687635	1.00[ASN][1000 genomes]
rs35920751	0.89[ASN][1000 genomes]
rs36068365	1.00[ASN][1000 genomes]
rs3800026	0.94[EUR][1000 genomes]
rs3924307	0.94[EUR][1000 genomes]
rs4072271	1.00[ASN][1000 genomes]
rs4074103	0.83[AFR][1000 genomes]
rs41267673	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271848	0.89[EUR][1000 genomes]
rs41271850	0.89[EUR][1000 genomes]
rs41271854	0.94[EUR][1000 genomes]
rs41271856	0.94[EUR][1000 genomes]
rs41271872	1.00[EUR][1000 genomes]
rs41271876	1.00[EUR][1000 genomes]
rs41271878	1.00[EUR][1000 genomes]
rs4133076	1.00[ASN][1000 genomes]
rs4256439	0.94[EUR][1000 genomes]
rs4275049	0.89[ASN][1000 genomes]
rs4288197	0.84[EUR][1000 genomes]
rs45442999	0.94[EUR][1000 genomes]
rs45553042	0.95[EUR][1000 genomes]
rs4574644	0.89[ASN][1000 genomes]
rs4640889	0.89[ASN][1000 genomes]
rs56094263	0.89[ASN][1000 genomes]
rs56196625	1.00[ASN][1000 genomes]
rs56991168	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs57289287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57350484	1.00[EUR][1000 genomes]
rs57392123	1.00[ASN][1000 genomes]
rs57488435	1.00[ASN][1000 genomes]
rs57790896	1.00[EUR][1000 genomes]
rs57822928	0.94[EUR][1000 genomes]
rs58487319	0.96[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs58565063	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58730144	0.94[EUR][1000 genomes]
rs59073430	1.00[ASN][1000 genomes]
rs59085778	0.89[ASN][1000 genomes]
rs59162324	0.89[ASN][1000 genomes]
rs59247267	0.89[ASN][1000 genomes]
rs59772940	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59864125	0.94[EUR][1000 genomes]
rs59889120	1.00[ASN][1000 genomes]
rs60360551	1.00[ASN][1000 genomes]
rs60498201	0.89[ASN][1000 genomes]
rs62621210	0.94[EUR][1000 genomes]
rs6459167	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6459168	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900572	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901176	1.00[ASN][1000 genomes]
rs6903517	0.85[EUR][1000 genomes]
rs6903815	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916813	1.00[ASN][1000 genomes]
rs6924375	1.00[ASN][1000 genomes]
rs6926134	0.89[ASN][1000 genomes]
rs6941626	1.00[EUR][1000 genomes]
rs73455767	0.94[EUR][1000 genomes]
rs73455782	0.94[EUR][1000 genomes]
rs73455797	0.97[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs73465854	0.94[EUR][1000 genomes]
rs73746926	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73746929	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73746930	1.00[ASN][1000 genomes]
rs73746931	1.00[ASN][1000 genomes]
rs73747826	0.89[EUR][1000 genomes]
rs73747832	0.89[EUR][1000 genomes]
rs73749935	0.94[EUR][1000 genomes]
rs73749942	0.94[EUR][1000 genomes]
rs73749948	0.94[EUR][1000 genomes]
rs73749949	0.94[EUR][1000 genomes]
rs7749100	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749437	1.00[ASN][1000 genomes]
rs7758867	1.00[CHD][hapmap]
rs7759479	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760503	1.00[CEU][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]
rs7760515	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7760542	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760701	1.00[EUR][1000 genomes]
rs7761027	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767128	1.00[ASN][1000 genomes]
rs7769014	0.94[EUR][1000 genomes]
rs7775134	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9370542	0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv432888	chr6:56507489-56560764	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56417000-56516400	Weak transcription	Pancreas	Pancrea
2	chr6:56441000-56524800	Weak transcription	Colonic Mucosa	Colon
3	chr6:56459000-56521000	Weak transcription	Spleen	Spleen
4	chr6:56480800-56536400	Weak transcription	Gastric	stomach
5	chr6:56482000-56518200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:56491600-56536600	Weak transcription	Fetal Brain Female	brain
7	chr6:56496600-56517000	Weak transcription	Fetal Brain Male	brain
8	chr6:56496800-56515000	Weak transcription	Fetal Kidney	kidney
9	chr6:56497800-56524800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:56499400-56516800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:56501800-56524600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:56505600-56522000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr6:56505600-56537400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:56506000-56516000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:56507400-56515800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:56508200-56520000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:56508800-56517000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr6:56509000-56514800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:56509200-56515400	Strong transcription	GM12878-XiMat	blood
20	chr6:56509400-56516600	Strong transcription	HSMM	muscle
21	chr6:56509800-56528200	Weak transcription	Esophagus	oesophagus
22	chr6:56510200-56516400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:56510400-56518200	Weak transcription	Brain Germinal Matrix	brain
24	chr6:56511600-56524600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:56511800-56517000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:56512200-56516400	Weak transcription	Ovary	ovary
27	chr6:56512400-56524600	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:56512600-56515200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:56512600-56534400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:56512800-56515000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:56513000-56515000	Enhancers	Brain Hippocampus Middle	brain
32	chr6:56513000-56534400	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:56513200-56517000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:56513200-56520200	Weak transcription	Fetal Stomach	stomach
35	chr6:56513200-56524400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:56513400-56515200	Enhancers	Fetal Intestine Small	intestine
37	chr6:56513400-56516000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:56513400-56516800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr6:56513400-56517000	Weak transcription	Adipose Nuclei	Adipose
40	chr6:56513600-56515000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr6:56513600-56515000	Enhancers	Duodenum Mucosa	Duodenum
42	chr6:56513600-56515000	Genic enhancers	Fetal Intestine Large	intestine
43	chr6:56513600-56515000	Enhancers	Small Intestine	intestine
44	chr6:56513600-56515000	Enhancers	Stomach Mucosa	stomach
45	chr6:56513600-56515200	Genic enhancers	HepG2	liver
46	chr6:56513600-56515600	Enhancers	NHEK	skin
47	chr6:56513600-56516800	Weak transcription	Psoas Muscle	Psoas
48	chr6:56513600-56520600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr6:56513800-56514800	Genic enhancers	HUVEC	blood vessel
50	chr6:56513800-56515000	Genic enhancers	NHLF	lung

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