Variant report

Variant	rs233476
Chromosome Location	chr6:4799385-4799386
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4775250..4779402-chr6:4796974..4799490,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236336	Chromatin interaction
ENSG00000153046	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1016877	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11967994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1265332	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1265333	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1265334	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1265335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13199417	0.91[CHB][hapmap]
rs13212871	0.91[CHB][hapmap]
rs17138856	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17138859	1.00[CHB][hapmap]
rs17138959	0.91[CHB][hapmap]
rs17138966	0.91[CHB][hapmap]
rs184588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2179269	0.81[EUR][1000 genomes]
rs2179270	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2326553	0.91[CHB][hapmap]
rs3748078	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61610972	0.85[EUR][1000 genomes]
rs62386574	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62386575	0.89[EUR][1000 genomes]
rs62386576	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62386577	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62386578	0.88[EUR][1000 genomes]
rs62386582	0.85[EUR][1000 genomes]
rs62386584	0.85[EUR][1000 genomes]
rs62386585	0.85[EUR][1000 genomes]
rs62386587	0.84[EUR][1000 genomes]
rs62386590	0.81[EUR][1000 genomes]
rs6910368	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs6918626	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs73362560	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs808593	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs808598	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs808600	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs808606	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs808607	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs808635	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs811251	0.91[CHB][hapmap]
rs9504254	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9504284	0.83[CHB][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	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1015888	chr6:4787784-4883663	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4787400-4808800	Weak transcription	Aorta	Aorta
2	chr6:4790000-4799800	Weak transcription	Ovary	ovary
3	chr6:4790200-4803200	Weak transcription	Pancreas	Pancrea
4	chr6:4790600-4801600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:4790800-4801200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:4790800-4801200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:4793600-4799600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:4793800-4799600	Weak transcription	Fetal Intestine Small	intestine
9	chr6:4793800-4799800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:4794800-4801800	Weak transcription	Psoas Muscle	Psoas
11	chr6:4794800-4802600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:4794800-4803200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:4794800-4803200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:4794800-4803600	Weak transcription	Esophagus	oesophagus
15	chr6:4794800-4804400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:4794800-4818800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:4795000-4799800	Weak transcription	Spleen	Spleen
18	chr6:4795000-4800800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:4795000-4802000	Weak transcription	Small Intestine	intestine
20	chr6:4795000-4802600	Weak transcription	Right Ventricle	heart
21	chr6:4795000-4803000	Weak transcription	Left Ventricle	heart
22	chr6:4795000-4803200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr6:4795000-4803200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:4795000-4803200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:4795000-4806200	Weak transcription	Gastric	stomach
26	chr6:4795200-4800200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:4795200-4800800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:4795200-4800800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr6:4795200-4801200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:4795200-4803400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr6:4795200-4803800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:4795200-4806600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:4795600-4799800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:4796000-4801000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr6:4796400-4799800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:4796600-4801600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:4797200-4799400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:4797400-4803200	Weak transcription	HSMM	muscle
39	chr6:4798000-4803200	Weak transcription	NHEK	skin
40	chr6:4798200-4799400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr6:4798200-4803600	Weak transcription	Hela-S3	cervix
42	chr6:4798200-4803600	Weak transcription	NHLF	lung
43	chr6:4798400-4801000	Weak transcription	K562	blood
44	chr6:4798400-4803200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:4798600-4799600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:4798600-4799600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:4798600-4800600	Enhancers	GM12878-XiMat	blood
48	chr6:4798600-4800800	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr6:4798600-4801200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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