Variant report

Variant	rs10947787
Chromosome Location	chr6:39174525-39174526
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:39168499..39172318-chr6:39172546..39178479,7	K562	blood:
2	chr6:39160875..39164831-chr6:39173251..39175892,4	K562	blood:
3	chr6:39169873..39175586-chr6:39175633..39178676,8	K562	blood:
4	chr6:39173383..39177261-chr6:39181456..39183734,4	K562	blood:
5	chr6:39161548..39165736-chr6:39172380..39175639,5	K562	blood:
6	chr6:39173237..39177206-chr6:39236026..39240576,5	MCF-7	breast:
7	chr6:39168413..39175988-chr6:39191555..39198727,12	K562	blood:
8	chr6:39173759..39176293-chr6:39187054..39189578,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10807202	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10947786	0.92[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs10947788	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10947789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12200013	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202900	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12207689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2033226	0.90[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714223	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4714224	0.89[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55818834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918122	0.90[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72851851	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10947787	TREM2	cis	parietal	SCAN
rs10947787	PRICKLE4	cis	parietal	SCAN
rs10947787	LHFPL5	cis	parietal	SCAN
rs10947787	TDRG1	cis	cerebellum	SCAN

Chromatin state (count:63 , 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	chr6:39156400-39177200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:39156800-39193400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:39163800-39192800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:39166400-39178200	Enhancers	Placenta	Placenta
6	chr6:39167400-39178600	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr6:39169400-39193600	Enhancers	Liver	Liver
8	chr6:39170000-39174600	Enhancers	Colonic Mucosa	Colon
9	chr6:39170000-39179400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr6:39170400-39176000	Weak transcription	Small Intestine	intestine
11	chr6:39170400-39179200	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr6:39170800-39175200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:39170800-39179200	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr6:39171000-39176000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr6:39171000-39179200	Genic enhancers	K562	blood
16	chr6:39171200-39174600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:39171400-39179200	Enhancers	Esophagus	oesophagus
18	chr6:39171600-39175000	Genic enhancers	Fetal Thymus	thymus
19	chr6:39172200-39174600	Genic enhancers	Fetal Intestine Large	intestine
20	chr6:39172200-39177000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:39172200-39177000	Weak transcription	NHEK	skin
22	chr6:39172400-39175200	Enhancers	Spleen	Spleen
23	chr6:39172400-39178600	Enhancers	Lung	lung
24	chr6:39172600-39175400	Strong transcription	Fetal Stomach	stomach
25	chr6:39172600-39177200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr6:39172800-39175000	Enhancers	Hela-S3	cervix
27	chr6:39173000-39176200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:39173000-39177600	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr6:39173200-39177000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:39173400-39174600	Enhancers	GM12878-XiMat	blood
31	chr6:39173400-39175000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:39173400-39175400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr6:39173400-39175800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:39173400-39177400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr6:39173600-39175200	Genic enhancers	Duodenum Mucosa	Duodenum
36	chr6:39173600-39175200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr6:39173800-39174600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:39173800-39177000	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr6:39173800-39177200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr6:39174000-39174600	Enhancers	HMEC	breast
41	chr6:39174000-39175000	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr6:39174000-39175000	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr6:39174000-39175200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr6:39174000-39175400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr6:39174000-39176000	Enhancers	Gastric	stomach
46	chr6:39174000-39176200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:39174000-39177000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr6:39174000-39177000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr6:39174000-39179000	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr6:39174000-39179200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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