Variant report

Variant	rs2144407
Chromosome Location	chr6:56505063-56505064
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56504232..56507291-chr6:56530802..56532619,3	MCF-7	breast:
2	chr6:56504038..56506002-chr6:56561278..56563980,2	MCF-7	breast:
3	chr6:56499630..56501199-chr6:56504985..56507404,2	MCF-7	breast:
4	chr6:56503799..56506491-chr6:56512573..56514282,2	MCF-7	breast:

Extended variants
information (count: 126 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1024196	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]
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	0.89[ASN][1000 genomes]
rs11970410	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
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]
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]
rs2180148	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207678	1.00[CEU][hapmap];0.87[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	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749437	1.00[ASN][1000 genomes]
rs7759479	1.00[CEU][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[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[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

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	chr6:56432800-56513600	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	chr6:56453000-56506800	Strong transcription	HSMM	muscle
7	chr6:56459000-56521000	Weak transcription	Spleen	Spleen
8	chr6:56460600-56513600	Weak transcription	Stomach Mucosa	stomach
9	chr6:56478400-56514600	Weak transcription	Lung	lung
10	chr6:56480600-56514600	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:56480800-56536400	Weak transcription	Gastric	stomach
12	chr6:56482000-56518200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:56483400-56512600	Weak transcription	Psoas Muscle	Psoas
14	chr6:56485000-56514400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:56485600-56507400	Weak transcription	Aorta	Aorta
16	chr6:56485800-56512400	Weak transcription	Fetal Stomach	stomach
17	chr6:56488800-56507200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:56490000-56513600	Strong transcription	Fetal Intestine Large	intestine
19	chr6:56490400-56507400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr6:56490800-56507400	Strong transcription	Liver	Liver
21	chr6:56491600-56536600	Weak transcription	Fetal Brain Female	brain
22	chr6:56496600-56517000	Weak transcription	Fetal Brain Male	brain
23	chr6:56496800-56515000	Weak transcription	Fetal Kidney	kidney
24	chr6:56497600-56506600	Weak transcription	Fetal Thymus	thymus
25	chr6:56497800-56524800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:56499400-56510000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr6:56499400-56511800	Weak transcription	Ovary	ovary
28	chr6:56499400-56516800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:56499600-56509200	Weak transcription	Right Ventricle	heart
30	chr6:56499600-56509400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:56500200-56509400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr6:56500600-56507200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr6:56500600-56509400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:56500600-56509400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr6:56500600-56509800	Weak transcription	Brain Germinal Matrix	brain
36	chr6:56500600-56514200	Weak transcription	Fetal Heart	heart
37	chr6:56500800-56513000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr6:56501000-56507800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:56501600-56506600	Weak transcription	HepG2	liver
40	chr6:56501600-56507800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr6:56501800-56507200	Weak transcription	Fetal Muscle Leg	muscle
42	chr6:56501800-56507400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:56501800-56524600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:56502000-56512400	Weak transcription	Fetal Intestine Small	intestine
45	chr6:56502600-56505400	Transcr. at gene 5' and 3'	NHEK	skin
46	chr6:56502600-56506200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:56502800-56505800	Transcr. at gene 5' and 3'	HMEC	breast
48	chr6:56503000-56505400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
49	chr6:56503000-56507600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:56503200-56505200	Active TSS	Thymus	Thymus

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