Variant report

Variant	rs1024196
Chromosome Location	chr6:56507489-56507490
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	chr6:56506621..56508645-chr6:56839158..56841779,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000219790	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs11961141	0.89[ASN][1000 genomes]
rs11961342	1.00[ASN][1000 genomes]
rs11963288	0.94[EUR][1000 genomes]
rs11966986	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11967796	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968575	1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs11970410	0.80[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[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2180148	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207678	1.00[CEU][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];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]
rs41267673	0.89[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	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];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	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];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	0.81[EUR][1000 genomes]
rs57289287	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57350484	0.94[AMR][1000 genomes];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	0.81[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	0.80[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	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901176	1.00[ASN][1000 genomes]
rs6903517	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6903815	0.95[AFR][1000 genomes];1.00[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	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73455767	0.94[EUR][1000 genomes]
rs73455782	0.94[EUR][1000 genomes]
rs73455797	0.81[EUR][1000 genomes]
rs73465854	0.94[EUR][1000 genomes]
rs73746926	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73746929	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	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.85[MKK][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749437	1.00[ASN][1000 genomes]
rs7758867	1.00[CHD][hapmap]
rs7759479	1.00[CEU][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760503	1.00[CEU][hapmap];0.80[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	0.83[AMR][1000 genomes];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];0.98[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]

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:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56417000-56516400	Weak transcription	Pancreas	Pancrea
2	chr6:56432800-56513600	Weak transcription	Small Intestine	intestine
3	chr6:56441000-56524800	Weak transcription	Colonic Mucosa	Colon
4	chr6:56451800-56514200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:56452200-56514600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:56459000-56521000	Weak transcription	Spleen	Spleen
7	chr6:56460600-56513600	Weak transcription	Stomach Mucosa	stomach
8	chr6:56478400-56514600	Weak transcription	Lung	lung
9	chr6:56480600-56514600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:56480800-56536400	Weak transcription	Gastric	stomach
11	chr6:56482000-56518200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:56483400-56512600	Weak transcription	Psoas Muscle	Psoas
13	chr6:56485000-56514400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr6:56485800-56512400	Weak transcription	Fetal Stomach	stomach
15	chr6:56490000-56513600	Strong transcription	Fetal Intestine Large	intestine
16	chr6:56491600-56536600	Weak transcription	Fetal Brain Female	brain
17	chr6:56496600-56517000	Weak transcription	Fetal Brain Male	brain
18	chr6:56496800-56515000	Weak transcription	Fetal Kidney	kidney
19	chr6:56497800-56524800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:56499400-56510000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr6:56499400-56511800	Weak transcription	Ovary	ovary
22	chr6:56499400-56516800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:56499600-56509200	Weak transcription	Right Ventricle	heart
24	chr6:56499600-56509400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:56500200-56509400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr6:56500600-56509400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:56500600-56509400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:56500600-56509800	Weak transcription	Brain Germinal Matrix	brain
29	chr6:56500600-56514200	Weak transcription	Fetal Heart	heart
30	chr6:56500800-56513000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr6:56501000-56507800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:56501600-56507800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:56501800-56524600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:56502000-56512400	Weak transcription	Fetal Intestine Small	intestine
35	chr6:56503000-56507600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:56503400-56507600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:56503600-56508000	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr6:56503600-56508200	Strong transcription	Fetal Lung	lung
39	chr6:56504000-56507800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr6:56504000-56508400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:56504200-56508000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:56505000-56508000	Strong transcription	Left Ventricle	heart
43	chr6:56505200-56509600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr6:56505400-56507600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:56505400-56507800	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr6:56505400-56508000	Active TSS	NHEK	skin
47	chr6:56505400-56509600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr6:56505400-56509600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr6:56505400-56510000	Weak transcription	Placenta	Placenta
50	chr6:56505400-56514600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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