Variant report

Variant	rs10844243
Chromosome Location	chr12:32713135-32713136
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10844246	1.00[JPT][hapmap]
rs11052092	1.00[JPT][hapmap]
rs16920058	1.00[JPT][hapmap]
rs17538032	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1909509	1.00[CHB][hapmap]
rs4569085	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73100112	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73100117	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7976053	0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1037224	chr12:32698189-32721994	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv541456	chr12:32698189-32721994	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv973958	chr12:32712509-32726963	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10844243	H3F3C	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32693000-32729600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:32698800-32719600	Weak transcription	Colonic Mucosa	Colon
3	chr12:32699600-32714800	Weak transcription	Fetal Intestine Large	intestine
4	chr12:32702000-32719400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:32702000-32719400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:32702800-32717200	Weak transcription	HUVEC	blood vessel
7	chr12:32703000-32717000	Weak transcription	HMEC	breast
8	chr12:32703000-32717200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:32703000-32719400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:32703200-32719000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:32704200-32719800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:32704600-32714600	Weak transcription	Fetal Heart	heart
13	chr12:32710000-32714400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:32710400-32715400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:32711000-32713400	Enhancers	Brain Substantia Nigra	brain
16	chr12:32711000-32713800	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr12:32711000-32714000	Enhancers	Primary B cells from peripheral blood	blood
18	chr12:32711200-32713400	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr12:32711200-32713400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:32711400-32713200	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr12:32711400-32713200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr12:32711400-32713200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:32711400-32713400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr12:32711400-32714800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr12:32711400-32714800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:32711400-32715400	Enhancers	HepG2	liver
27	chr12:32711600-32713200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr12:32711600-32713400	Enhancers	Brain Angular Gyrus	brain
29	chr12:32711800-32713200	Weak transcription	Small Intestine	intestine
30	chr12:32711800-32714600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr12:32711800-32714800	Weak transcription	Pancreas	Pancrea
32	chr12:32711800-32714800	Weak transcription	HSMM	muscle
33	chr12:32711800-32717000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr12:32711800-32719800	Weak transcription	Gastric	stomach
35	chr12:32711800-32724800	Weak transcription	Fetal Brain Male	brain
36	chr12:32712000-32713800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr12:32712000-32714600	Weak transcription	HSMMtube	muscle
38	chr12:32712000-32714800	Weak transcription	Fetal Stomach	stomach
39	chr12:32712000-32717000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr12:32712200-32713400	Enhancers	Fetal Lung	lung
41	chr12:32712200-32717000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr12:32712200-32719000	Weak transcription	Aorta	Aorta
43	chr12:32712400-32713200	Enhancers	Brain Hippocampus Middle	brain
44	chr12:32712400-32713400	Enhancers	Muscle Satellite Cultured Cells	--
45	chr12:32712400-32713800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:32712600-32713200	Enhancers	H1 Cell Line	embryonic stem cell
47	chr12:32712600-32713200	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr12:32712600-32713200	Enhancers	GM12878-XiMat	blood
49	chr12:32712600-32713200	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr12:32712600-32713200	Enhancers	NHDF-Ad	bronchial

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