Variant report

Variant	rs11970410
Chromosome Location	chr6:56521751-56521752
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	chr6:56517201..56519580-chr6:56519629..56522798,3	MCF-7	breast:
2	chr6:56521338..56523771-chr6:56524136..56525857,2	K562	blood:

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1024196	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11751914	0.93[YRI][hapmap]
rs11961342	0.90[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];0.90[ASN][1000 genomes]
rs11967796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11968575	1.00[CHD][hapmap]
rs11970648	1.00[CHD][hapmap]
rs13191164	0.90[ASN][1000 genomes]
rs13205013	0.90[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	0.81[ASN][1000 genomes]
rs16888096	0.90[ASN][1000 genomes]
rs16888106	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16888118	0.90[ASN][1000 genomes]
rs16888124	0.90[ASN][1000 genomes]
rs16888128	0.90[ASN][1000 genomes]
rs16888130	0.90[ASN][1000 genomes]
rs16888133	0.90[ASN][1000 genomes]
rs16888171	1.00[CHD][hapmap]
rs2144407	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2180148	1.00[EUR][1000 genomes];0.90[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]
rs34138864	0.81[ASN][1000 genomes]
rs34429594	0.90[ASN][1000 genomes]
rs34724718	0.90[ASN][1000 genomes]
rs35206656	0.90[ASN][1000 genomes]
rs35637749	0.90[ASN][1000 genomes]
rs35687635	0.90[ASN][1000 genomes]
rs36068365	0.90[ASN][1000 genomes]
rs3800026	0.94[EUR][1000 genomes]
rs3924307	0.94[EUR][1000 genomes]
rs4072271	0.90[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];0.90[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	0.90[ASN][1000 genomes]
rs4256439	0.94[EUR][1000 genomes]
rs4288197	0.84[EUR][1000 genomes]
rs45442999	0.94[EUR][1000 genomes]
rs45553042	0.95[EUR][1000 genomes]
rs56196625	0.90[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];0.90[ASN][1000 genomes]
rs57350484	1.00[EUR][1000 genomes]
rs57392123	0.90[ASN][1000 genomes]
rs57488435	0.90[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];0.90[ASN][1000 genomes]
rs58730144	0.94[EUR][1000 genomes]
rs59073430	0.90[ASN][1000 genomes]
rs59772940	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59864125	0.94[EUR][1000 genomes]
rs59889120	0.90[ASN][1000 genomes]
rs60360551	0.90[ASN][1000 genomes]
rs62621210	0.94[EUR][1000 genomes]
rs6459167	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6459168	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6900572	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6901176	0.90[ASN][1000 genomes]
rs6903517	0.85[EUR][1000 genomes]
rs6903815	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6916813	0.90[ASN][1000 genomes]
rs6924375	0.90[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];0.90[ASN][1000 genomes]
rs73746929	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73746930	0.90[ASN][1000 genomes]
rs73746931	0.90[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];0.90[ASN][1000 genomes]
rs7749437	0.90[ASN][1000 genomes]
rs7758867	1.00[CHD][hapmap]
rs7759479	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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];0.90[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];0.90[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];0.90[ASN][1000 genomes]
rs7760701	1.00[EUR][1000 genomes]
rs7761027	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7767128	0.90[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:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56441000-56524800	Weak transcription	Colonic Mucosa	Colon
2	chr6:56480800-56536400	Weak transcription	Gastric	stomach
3	chr6:56491600-56536600	Weak transcription	Fetal Brain Female	brain
4	chr6:56497800-56524800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:56501800-56524600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:56505600-56522000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr6:56505600-56537400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:56509800-56528200	Weak transcription	Esophagus	oesophagus
9	chr6:56511600-56524600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:56512400-56524600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr6:56512600-56534400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:56513000-56534400	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:56513200-56524400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr6:56514800-56537000	Weak transcription	Lung	lung
15	chr6:56515000-56524200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:56515000-56524600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:56515000-56534400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:56515800-56524400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr6:56516600-56524800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:56517400-56524400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr6:56517400-56524600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:56517400-56536400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:56518200-56521800	Enhancers	A549	lung
24	chr6:56518200-56522400	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr6:56518200-56522400	Weak transcription	HSMMtube	muscle
26	chr6:56518200-56524600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:56518200-56524600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:56518200-56524600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:56518200-56524800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:56518600-56524600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:56518600-56524600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:56519000-56523200	Weak transcription	GM12878-XiMat	blood
33	chr6:56519000-56524600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:56519000-56524800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:56519000-56524800	Weak transcription	NH-A	brain
36	chr6:56519200-56523000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr6:56519800-56522000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:56519800-56523000	Enhancers	Primary hematopoietic stem cells	blood
39	chr6:56520000-56522200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:56520000-56522400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:56520000-56522400	Enhancers	Brain Anterior Caudate	brain
42	chr6:56520000-56522400	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr6:56520000-56526400	Enhancers	Brain Substantia Nigra	brain
44	chr6:56520000-56526800	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr6:56520000-56526800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:56520200-56522000	Enhancers	Adipose Nuclei	Adipose
47	chr6:56520200-56524600	Enhancers	NHEK	skin
48	chr6:56520200-56527400	Enhancers	Brain Cingulate Gyrus	brain
49	chr6:56520400-56521800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:56520400-56522000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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