Variant report

Variant	rs2180106
Chromosome Location	chr6:38560215-38560216
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38554358..38556905-chr6:38558804..38560728,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000217227	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13213112	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219252	1.00[CHD][hapmap]
rs17543178	1.00[CHB][hapmap]
rs17544359	1.00[CHB][hapmap]
rs2748174	1.00[CHB][hapmap]
rs34841627	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34958830	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2180106	BYSL	cis	cerebellum	SCAN
rs2180106	C6orf130	cis	parietal	SCAN
rs2180106	KCNK5	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38523000-38571600	Weak transcription	HSMMtube	muscle
2	chr6:38534400-38561600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr6:38535800-38564000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:38535800-38578200	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:38536800-38566400	Weak transcription	Pancreas	Pancrea
6	chr6:38538000-38566800	Weak transcription	Esophagus	oesophagus
7	chr6:38538600-38561800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr6:38538600-38562000	Weak transcription	Brain Germinal Matrix	brain
9	chr6:38539800-38562800	Weak transcription	Fetal Thymus	thymus
10	chr6:38540400-38561600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr6:38540400-38567800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr6:38540400-38569200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:38541000-38565200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:38541400-38568600	Weak transcription	Spleen	Spleen
15	chr6:38541600-38567000	Weak transcription	Small Intestine	intestine
16	chr6:38542000-38563400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:38545000-38561400	Weak transcription	Psoas Muscle	Psoas
18	chr6:38545400-38566000	Weak transcription	Colonic Mucosa	Colon
19	chr6:38546200-38563800	Weak transcription	Gastric	stomach
20	chr6:38547400-38565400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:38547400-38566600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:38548200-38561600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:38548200-38563800	Weak transcription	Brain Substantia Nigra	brain
24	chr6:38548200-38570800	Weak transcription	Fetal Kidney	kidney
25	chr6:38549000-38570800	Weak transcription	Fetal Intestine Small	intestine
26	chr6:38553400-38562200	Strong transcription	Primary T cells from cord blood	blood
27	chr6:38555000-38565800	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr6:38556000-38563800	Weak transcription	Fetal Heart	heart
29	chr6:38556000-38580400	Weak transcription	Ovary	ovary
30	chr6:38556200-38567400	Weak transcription	Lung	lung
31	chr6:38556800-38560400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:38556800-38563400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:38557000-38562400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr6:38557200-38561000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:38557200-38562000	Weak transcription	HUVEC	blood vessel
36	chr6:38557400-38561600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:38557400-38571800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr6:38557400-38571800	Weak transcription	NHDF-Ad	bronchial
39	chr6:38557400-38578000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:38557600-38560600	Strong transcription	HSMM	muscle
41	chr6:38557800-38562800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr6:38557800-38571600	Weak transcription	HMEC	breast
43	chr6:38557800-38572000	Weak transcription	NHLF	lung
44	chr6:38558200-38562400	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr6:38558200-38564000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr6:38558200-38565000	Weak transcription	Fetal Brain Male	brain
47	chr6:38558400-38560600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:38558400-38562200	Strong transcription	Adipose Nuclei	Adipose
49	chr6:38558400-38566000	Strong transcription	Primary B cells from cord blood	blood
50	chr6:38558600-38561000	Strong transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links