Variant report

Variant	rs10456100
Chromosome Location	chr6:39183470-39183471
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:39177427..39182769-chr6:39182785..39188256,10	K562	blood:
2	chr6:39181537..39183525-chr6:39264253..39266272,2	K562	blood:
3	chr6:39173383..39177261-chr6:39181456..39183734,4	K562	blood:

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2561396	0.80[EUR][1000 genomes]
rs2815116	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs733701	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9394578	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]

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	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Migraine	23793025	GWAS catalog

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39150600-39193800	Genic enhancers	Fetal Intestine Small	intestine
2	chr6:39156800-39193400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:39163800-39192800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:39169400-39193600	Enhancers	Liver	Liver
5	chr6:39174200-39195000	Enhancers	Stomach Mucosa	stomach
6	chr6:39177600-39186400	Weak transcription	Primary T cells from cord blood	blood
7	chr6:39178000-39193400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:39178200-39184400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:39178200-39185000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr6:39178200-39185000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:39178200-39185200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:39178200-39186600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:39178400-39185000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr6:39178400-39185200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:39178600-39193200	Weak transcription	Thymus	Thymus
16	chr6:39178800-39184800	Genic enhancers	Fetal Intestine Large	intestine
17	chr6:39179000-39186200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:39179000-39186800	Genic enhancers	Fetal Thymus	thymus
19	chr6:39179200-39184400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr6:39179200-39186200	Weak transcription	Small Intestine	intestine
21	chr6:39180000-39184000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr6:39180000-39184600	Strong transcription	Fetal Stomach	stomach
23	chr6:39180200-39184200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:39180200-39184600	Genic enhancers	Duodenum Mucosa	Duodenum
25	chr6:39180400-39183600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:39181000-39184600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:39181200-39183600	Enhancers	Esophagus	oesophagus
28	chr6:39181600-39185000	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr6:39181800-39189400	Genic enhancers	K562	blood
30	chr6:39182000-39183600	Enhancers	Fetal Kidney	kidney
31	chr6:39182000-39183600	Enhancers	Ovary	ovary
32	chr6:39182000-39183600	Flanking Active TSS	A549	lung
33	chr6:39182000-39185000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr6:39182000-39186800	Enhancers	Lung	lung
35	chr6:39182200-39183600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:39182200-39190000	Enhancers	Pancreas	Pancrea
37	chr6:39182200-39195200	Enhancers	Fetal Lung	lung
38	chr6:39182400-39185000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:39182400-39185000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:39182600-39183600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr6:39182600-39183600	Enhancers	Spleen	Spleen
42	chr6:39182800-39183600	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr6:39182800-39183800	Enhancers	Primary T cells fromperipheralblood	blood
44	chr6:39182800-39183800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:39183000-39183600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:39183000-39183600	Enhancers	Gastric	stomach
47	chr6:39183000-39183800	Enhancers	Primary hematopoietic stem cells	blood
48	chr6:39183000-39184600	Enhancers	GM12878-XiMat	blood
49	chr6:39183000-39184800	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr6:39183000-39185000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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