Variant report

Variant	rs233477
Chromosome Location	chr6:4796998-4796999
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4779066..4782355-chr6:4795807..4798992,3	K562	blood:
2	chr6:4775250..4779402-chr6:4796974..4799490,3	MCF-7	breast:
3	chr6:4788250..4792483-chr6:4794003..4797255,3	MCF-7	breast:
4	chr6:4796490..4799008-chr6:4800485..4802144,2	K562	blood:
5	chr6:4773227..4775902-chr6:4794032..4797060,3	K562	blood:

Variant related genes	Relation type
ENSG00000236336	Chromatin interaction
ENSG00000153046	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1265336	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1883327	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs233479	0.82[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[ASN][1000 genomes]
rs55653939	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6925763	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73364556	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7747591	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs808615	0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs808622	0.87[ASW][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];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	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:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4781600-4797800	Weak transcription	Hela-S3	cervix
2	chr6:4782000-4797800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:4787400-4808800	Weak transcription	Aorta	Aorta
4	chr6:4790000-4799800	Weak transcription	Ovary	ovary
5	chr6:4790200-4803200	Weak transcription	Pancreas	Pancrea
6	chr6:4790600-4801600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:4790800-4801200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:4790800-4801200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr6:4791000-4797200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:4791800-4797800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:4792200-4797600	Weak transcription	NH-A	brain
12	chr6:4793600-4799600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:4793800-4798600	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr6:4793800-4799600	Weak transcription	Fetal Intestine Small	intestine
15	chr6:4793800-4799800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:4794200-4798200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr6:4794800-4798400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr6:4794800-4801800	Weak transcription	Psoas Muscle	Psoas
19	chr6:4794800-4802600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:4794800-4803200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:4794800-4803200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:4794800-4803600	Weak transcription	Esophagus	oesophagus
23	chr6:4794800-4804400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:4794800-4818800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr6:4795000-4797200	Weak transcription	NHLF	lung
26	chr6:4795000-4797800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:4795000-4799800	Weak transcription	Spleen	Spleen
28	chr6:4795000-4800800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr6:4795000-4802000	Weak transcription	Small Intestine	intestine
30	chr6:4795000-4802600	Weak transcription	Right Ventricle	heart
31	chr6:4795000-4803000	Weak transcription	Left Ventricle	heart
32	chr6:4795000-4803200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:4795000-4803200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:4795000-4803200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:4795000-4806200	Weak transcription	Gastric	stomach
36	chr6:4795200-4798000	Weak transcription	K562	blood
37	chr6:4795200-4800200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr6:4795200-4800800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:4795200-4800800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:4795200-4801200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:4795200-4803400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr6:4795200-4803800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:4795200-4806600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:4795600-4799800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:4795800-4797400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:4796000-4797800	Weak transcription	NHEK	skin
47	chr6:4796000-4801000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr6:4796200-4798600	Weak transcription	GM12878-XiMat	blood
49	chr6:4796400-4799800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:4796600-4798000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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