Variant report

Variant	rs6457824
Chromosome Location	chr6:35428900-35428901
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35427041..35429819-chr6:35457117..35459807,2	K562	blood:
2	chr6:35419142..35422512-chr6:35424570..35429105,6	MCF-7	breast:
3	chr6:35424729..35431814-chr6:35432688..35440099,20	K562	blood:
4	chr6:35427059..35428930-chr6:35434282..35437196,3	MCF-7	breast:
5	chr6:35423275..35426107-chr6:35428625..35431307,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198755	Chromatin interaction
ENSG00000112039	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11553979	0.93[ASN][1000 genomes]
rs11962317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16876572	1.00[CEU][hapmap]
rs16876584	0.93[ASN][1000 genomes]
rs16876587	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3800376	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs41271261	0.93[ASN][1000 genomes]
rs45479891	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6457822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6457823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6914178	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6926662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6927202	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6927367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7746718	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7767821	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7768070	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9462087	0.97[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9462088	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9462089	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9470027	0.89[ASN][1000 genomes]
rs9470029	0.86[YRI][hapmap]
rs9470030	0.89[ASN][1000 genomes]
rs9470033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9470035	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9470038	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830641	chr6:35282534-35440603	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
2	nsv528351	chr6:35377922-35465786	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
3	nsv885799	chr6:35378778-35442397	Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
4	nsv462908	chr6:35378778-35457396	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
5	nsv602910	chr6:35378778-35457396	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
6	nsv519370	chr6:35378778-35537406	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases
7	nsv969390	chr6:35428276-35434702	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35421000-35435400	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:35421200-35435200	Weak transcription	Brain Angular Gyrus	brain
3	chr6:35421200-35435400	Weak transcription	Brain Anterior Caudate	brain
4	chr6:35421400-35435400	Weak transcription	Colonic Mucosa	Colon
5	chr6:35421400-35435400	Weak transcription	Fetal Kidney	kidney
6	chr6:35421400-35435400	Weak transcription	Pancreas	Pancrea
7	chr6:35421600-35433800	Weak transcription	HUVEC	blood vessel
8	chr6:35421600-35435200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr6:35421600-35435200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr6:35421600-35435400	Weak transcription	A549	lung
11	chr6:35421600-35435400	Weak transcription	NH-A	brain
12	chr6:35421800-35431000	Weak transcription	Liver	Liver
13	chr6:35422000-35430200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:35422200-35435200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:35422200-35435400	Weak transcription	Small Intestine	intestine
16	chr6:35422400-35430200	Weak transcription	HSMM	muscle
17	chr6:35422400-35434800	Strong transcription	Fetal Intestine Small	intestine
18	chr6:35422600-35429200	Strong transcription	Dnd41	blood
19	chr6:35422600-35435400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:35422800-35431000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:35422800-35434800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:35422800-35434800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:35422800-35435200	Weak transcription	Fetal Thymus	thymus
24	chr6:35422800-35435400	Weak transcription	Fetal Brain Male	brain
25	chr6:35422800-35435600	Weak transcription	Right Atrium	heart
26	chr6:35423000-35435200	Weak transcription	Fetal Heart	heart
27	chr6:35423000-35435200	Strong transcription	Fetal Stomach	stomach
28	chr6:35423000-35435400	Weak transcription	NHDF-Ad	bronchial
29	chr6:35423200-35429200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:35423200-35432200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:35423200-35435200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:35423400-35429000	Strong transcription	Spleen	Spleen
33	chr6:35423400-35429200	Strong transcription	Ovary	ovary
34	chr6:35423400-35429400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:35423400-35430800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr6:35423400-35431400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr6:35423400-35431400	Strong transcription	Brain Germinal Matrix	brain
38	chr6:35423400-35431400	Strong transcription	Fetal Lung	lung
39	chr6:35423400-35431800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:35423400-35431800	Strong transcription	Fetal Intestine Large	intestine
41	chr6:35423400-35432000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:35423400-35432000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:35423400-35434600	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr6:35423400-35434800	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr6:35423400-35435200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:35423400-35435400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:35423600-35429200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr6:35423600-35429400	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr6:35424000-35435600	Weak transcription	Psoas Muscle	Psoas
50	chr6:35424200-35435400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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