Variant report

Variant	rs2797790
Chromosome Location	chr6:37447075-37447076
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37441028..37444169-chr6:37445385..37448587,3	MCF-7	breast:
2	chr6:37446453..37448287-chr6:37452979..37455187,2	MCF-7	breast:
3	chr6:37444354..37450261-chr6:37451286..37455412,6	K562	blood:

Variant related genes	Relation type
ENSG00000137200	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10692	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11756941	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12212090	0.92[ASN][1000 genomes]
rs1224127	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1224128	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1224129	0.84[ASN][1000 genomes]
rs1812186	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2252920	0.87[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2646926	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2646933	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2646934	0.83[JPT][hapmap]
rs2776881	0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap]
rs2776906	0.86[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2776908	0.95[ASN][1000 genomes]
rs2776910	0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2776911	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2776916	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4257849	0.86[ASN][1000 genomes]
rs62406516	0.99[ASN][1000 genomes]
rs756202	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs904251	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs931649	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2797790	RNF8	cis	cerebellum	SCAN
rs2797790	FTSJD2	cis	parietal	SCAN
rs2797790	C6orf129	cis	parietal	SCAN
rs2797790	RP1-153P14.5	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37424600-37451600	Strong transcription	Fetal Thymus	thymus
2	chr6:37431800-37447200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:37435800-37452000	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr6:37436200-37457200	Strong transcription	Primary T cells from cord blood	blood
5	chr6:37436400-37448600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr6:37436400-37454600	Strong transcription	Thymus	Thymus
7	chr6:37436600-37452000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:37436600-37452000	Strong transcription	Fetal Lung	lung
9	chr6:37436800-37448600	Strong transcription	Primary B cells from cord blood	blood
10	chr6:37436800-37451800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr6:37436800-37452200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:37437000-37451800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:37437400-37448600	Strong transcription	Fetal Stomach	stomach
14	chr6:37437400-37454400	Strong transcription	Dnd41	blood
15	chr6:37437600-37451400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:37437600-37451800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr6:37437600-37452000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr6:37437800-37451600	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr6:37438000-37451600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:37438000-37454600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:37438200-37449000	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr6:37438200-37449600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:37438200-37451600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:37438200-37451600	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr6:37438200-37451800	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:37438200-37452000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr6:37438200-37452000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr6:37438200-37452400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:37438200-37454400	Strong transcription	Placenta	Placenta
30	chr6:37438400-37448200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr6:37438400-37448200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:37438400-37448600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:37438400-37451000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:37438400-37451200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr6:37438400-37451400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr6:37438400-37451400	Strong transcription	Colonic Mucosa	Colon
37	chr6:37438400-37451600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
38	chr6:37438400-37451800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr6:37438400-37452000	Strong transcription	Aorta	Aorta
40	chr6:37438400-37452000	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr6:37438400-37453400	Strong transcription	Fetal Intestine Large	intestine
42	chr6:37438600-37448200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:37438600-37449200	Strong transcription	Brain Cingulate Gyrus	brain
44	chr6:37438600-37451800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:37438600-37453000	Strong transcription	Lung	lung
46	chr6:37438600-37454600	Strong transcription	Spleen	Spleen
47	chr6:37438800-37448000	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:37439000-37447600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:37439000-37448200	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:37439000-37448200	Strong transcription	Fetal Brain Female	brain

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