Variant report

Variant	rs879482
Chromosome Location	chr6:37457663-37457664
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37454869..37462977-chr6:37463391..37469245,23	K562	blood:
2	chr6:37440015..37443370-chr6:37454781..37457774,3	K562	blood:
3	chr6:37348994..37349906-chr6:37457240..37457994,2	K562	blood:
4	chr6:37448409..37450836-chr6:37456466..37458234,2	MCF-7	breast:
5	chr6:37430006..37431711-chr6:37457108..37458826,2	K562	blood:

Variant related genes	Relation type
ENSG00000137200	Chromatin interaction
ENSG00000198937	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12529271	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16889848	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17572459	0.82[CHB][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28385585	0.81[AFR][1000 genomes]
rs55800130	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55979453	0.83[AMR][1000 genomes]
rs58351141	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73427657	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs904251	0.81[LWK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752124	chr6:37416219-37680622	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	esv3413317	chr6:37456674-37460972	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs879482	NCR2	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37442000-37458800	Weak transcription	HUVEC	blood vessel
2	chr6:37443600-37466600	Weak transcription	A549	lung
3	chr6:37446800-37466600	Weak transcription	Hela-S3	cervix
4	chr6:37447600-37466800	Weak transcription	HSMM	muscle
5	chr6:37448400-37466800	Weak transcription	Stomach Mucosa	stomach
6	chr6:37448800-37457800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:37449600-37459800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:37450200-37467200	Weak transcription	Small Intestine	intestine
9	chr6:37451000-37457800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:37451200-37458400	Weak transcription	Brain Angular Gyrus	brain
11	chr6:37451200-37459600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:37451200-37459800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:37451400-37457800	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:37451400-37458600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:37451400-37459200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:37451400-37465600	Weak transcription	Colonic Mucosa	Colon
17	chr6:37451600-37458400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:37451600-37466800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr6:37451600-37467000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr6:37451800-37459000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:37451800-37459000	Weak transcription	Liver	Liver
22	chr6:37451800-37462400	Enhancers	Fetal Brain Male	brain
23	chr6:37451800-37466600	Weak transcription	Primary B cells from cord blood	blood
24	chr6:37451800-37466800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:37452000-37457800	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:37452000-37459600	Weak transcription	Esophagus	oesophagus
27	chr6:37452000-37459800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr6:37452000-37460800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:37452000-37460800	Weak transcription	Ovary	ovary
30	chr6:37452000-37462200	Weak transcription	Aorta	Aorta
31	chr6:37452000-37466600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr6:37452000-37466800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:37452200-37466800	Weak transcription	NHLF	lung
34	chr6:37452400-37457800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:37452600-37461000	Weak transcription	Gastric	stomach
36	chr6:37452600-37466800	Weak transcription	NHDF-Ad	bronchial
37	chr6:37452600-37466800	Weak transcription	Osteobl	bone
38	chr6:37453000-37458200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr6:37453000-37459000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:37453200-37458600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr6:37453200-37466600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr6:37453400-37458000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:37453400-37466800	Weak transcription	Fetal Intestine Large	intestine
44	chr6:37454200-37460200	Enhancers	Brain Germinal Matrix	brain
45	chr6:37454200-37460400	Enhancers	Fetal Brain Female	brain
46	chr6:37454600-37464400	Weak transcription	K562	blood
47	chr6:37455000-37461000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr6:37455000-37461800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr6:37455600-37460800	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr6:37455600-37461800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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