Variant report

Variant	rs2776916
Chromosome Location	chr6:37462040-37462041
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37460921..37462916-chr6:37482767..37484311,2	MCF-7	breast:
2	chr6:37454869..37462977-chr6:37463391..37469245,23	K562	blood:
3	chr6:37435201..37437233-chr6:37461003..37462712,2	K562	blood:
4	chr6:37458120..37463201-chr6:37463391..37469475,12	K562	blood:
5	chr6:37461034..37463447-chr6:37474954..37477382,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204110	Chromatin interaction
ENSG00000198937	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10692	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11756941	0.85[ASN][1000 genomes]
rs12212090	0.90[ASN][1000 genomes]
rs1224127	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1224128	0.83[ASN][1000 genomes]
rs1224129	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1812186	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252920	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2646926	0.86[ASN][1000 genomes]
rs2646933	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2776873	0.81[EUR][1000 genomes]
rs2776881	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2776906	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2776908	0.92[ASN][1000 genomes]
rs2776910	0.92[ASN][1000 genomes]
rs2776911	0.94[ASN][1000 genomes]
rs2797790	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4257849	0.85[ASN][1000 genomes]
rs62406516	0.96[ASN][1000 genomes]
rs756202	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs904251	0.99[ASN][1000 genomes]
rs931649	0.96[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2776916	RP1-153P14.8	cis	Whole Blood	GTEx
rs2776916	RP1-153P14.5	cis	Whole Blood	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37443600-37466600	Weak transcription	A549	lung
2	chr6:37446800-37466600	Weak transcription	Hela-S3	cervix
3	chr6:37447600-37466800	Weak transcription	HSMM	muscle
4	chr6:37448400-37466800	Weak transcription	Stomach Mucosa	stomach
5	chr6:37450200-37467200	Weak transcription	Small Intestine	intestine
6	chr6:37451400-37465600	Weak transcription	Colonic Mucosa	Colon
7	chr6:37451600-37466800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:37451600-37467000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:37451800-37462400	Enhancers	Fetal Brain Male	brain
10	chr6:37451800-37466600	Weak transcription	Primary B cells from cord blood	blood
11	chr6:37451800-37466800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:37452000-37462200	Weak transcription	Aorta	Aorta
13	chr6:37452000-37466600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr6:37452000-37466800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:37452200-37466800	Weak transcription	NHLF	lung
16	chr6:37452600-37466800	Weak transcription	NHDF-Ad	bronchial
17	chr6:37452600-37466800	Weak transcription	Osteobl	bone
18	chr6:37453200-37466600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:37453400-37466800	Weak transcription	Fetal Intestine Large	intestine
20	chr6:37454600-37464400	Weak transcription	K562	blood
21	chr6:37455600-37463800	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr6:37456200-37464400	Enhancers	Primary T cells fromperipheralblood	blood
23	chr6:37456400-37467000	Weak transcription	Fetal Intestine Small	intestine
24	chr6:37456600-37466800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr6:37457400-37463000	Enhancers	GM12878-XiMat	blood
26	chr6:37458000-37466200	Weak transcription	Lung	lung
27	chr6:37458000-37466800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:37458200-37466800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr6:37458400-37466200	Weak transcription	HepG2	liver
30	chr6:37459000-37466800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr6:37459400-37466600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:37459400-37466800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:37459400-37466800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:37459400-37467000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:37459600-37466600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:37459800-37466600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:37459800-37466800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:37460000-37464600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr6:37460000-37466600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:37460000-37466600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:37460000-37466800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:37460000-37466800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr6:37460000-37467000	Weak transcription	Right Atrium	heart
44	chr6:37460400-37465600	Weak transcription	Primary T cells from cord blood	blood
45	chr6:37460400-37466600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr6:37460400-37466600	Weak transcription	Right Ventricle	heart
47	chr6:37460400-37466800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr6:37460600-37464400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr6:37460600-37464800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr6:37460600-37466600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links