Variant report

Variant	rs2176870
Chromosome Location	chr15:43436410-43436411
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:43436300-43436450	GM06990	blood:	n/a	n/a
2	POLR2A	chr15:43436216-43436721	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr15:43435521-43437017	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43424687..43428034-chr15:43433131..43438698,7	K562	blood:
2	chr15:43436161..43437895-chr15:43441050..43442861,2	K562	blood:

Variant related genes	Relation type
TMEM62	TF binding region
ENSG00000137842	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12898353	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12912837	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16957422	0.89[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs28414375	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28581361	0.81[ASN][1000 genomes]
rs35540074	0.83[EUR][1000 genomes]
rs4924705	0.83[CHD][hapmap];0.88[JPT][hapmap]
rs4924707	0.86[CEU][hapmap]
rs538218	0.89[LWK][hapmap]
rs540587	0.83[YRI][hapmap]
rs542036	0.80[GIH][hapmap]
rs579178	0.86[CEU][hapmap]
rs7176957	0.89[CHD][hapmap];0.88[JPT][hapmap]
rs9796684	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv515876	chr15:43116906-43445305	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv569240	chr15:43201109-43445305	Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv569242	chr15:43210030-43445305	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv904136	chr15:43257475-43482127	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv904139	chr15:43268970-43482127	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv904144	chr15:43276345-43482127	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	esv1802035	chr15:43370916-43487742	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2176870	PLCB2	cis	parietal	SCAN
rs2176870	TGM5	cis	lymphoblastoid	seeQTL
rs2176870	CCNDBP1	cis	multi-tissue	Pritchard
rs2176870	ZNF690	cis	multi-tissue	Pritchard
rs2176870	BMF	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43426600-43442200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:43426800-43455800	Weak transcription	Fetal Lung	lung
3	chr15:43426800-43465400	Weak transcription	Psoas Muscle	Psoas
4	chr15:43427000-43440600	Weak transcription	Fetal Heart	heart
5	chr15:43427000-43442200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr15:43427000-43442200	Weak transcription	NH-A	brain
7	chr15:43427600-43475000	Weak transcription	Stomach Mucosa	stomach
8	chr15:43427800-43448400	Weak transcription	Fetal Kidney	kidney
9	chr15:43428000-43445600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr15:43429000-43436800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:43429400-43444400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:43430400-43436800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:43430400-43441000	Weak transcription	HSMMtube	muscle
14	chr15:43430600-43441200	Weak transcription	Hela-S3	cervix
15	chr15:43430600-43442000	Weak transcription	HMEC	breast
16	chr15:43431000-43442000	Weak transcription	Fetal Thymus	thymus
17	chr15:43432200-43441000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:43432200-43446400	Weak transcription	Small Intestine	intestine
19	chr15:43433000-43436600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:43433000-43441000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:43433200-43436800	Weak transcription	NHDF-Ad	bronchial
22	chr15:43433200-43441000	Weak transcription	Colonic Mucosa	Colon
23	chr15:43433200-43460600	Weak transcription	Right Ventricle	heart
24	chr15:43433400-43438400	Weak transcription	Brain Anterior Caudate	brain
25	chr15:43433400-43438600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr15:43433400-43440800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr15:43433400-43441200	Weak transcription	Brain Angular Gyrus	brain
28	chr15:43433400-43441200	Weak transcription	Lung	lung
29	chr15:43433400-43441800	Weak transcription	Aorta	Aorta
30	chr15:43433400-43441800	Weak transcription	Osteobl	bone
31	chr15:43433400-43442000	Weak transcription	NHLF	lung
32	chr15:43433400-43442400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:43433400-43442400	Weak transcription	NHEK	skin
34	chr15:43433400-43443600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr15:43433400-43446000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr15:43433400-43446000	Weak transcription	Ovary	ovary
37	chr15:43433400-43451800	Weak transcription	Esophagus	oesophagus
38	chr15:43433400-43452600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:43433400-43460400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:43433400-43460400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:43433400-43460400	Weak transcription	Spleen	Spleen
42	chr15:43433400-43460600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:43433400-43460600	Weak transcription	Gastric	stomach
44	chr15:43433400-43467600	Weak transcription	HSMM	muscle
45	chr15:43433600-43438200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr15:43433600-43441000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:43433600-43441200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:43433600-43442400	Weak transcription	HepG2	liver
49	chr15:43433600-43442600	Weak transcription	Left Ventricle	heart
50	chr15:43433600-43444600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links