Variant report

Variant	rs12076549
Chromosome Location	chr1:92201699-92201700
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	chr1:92198152..92200213-chr1:92201193..92206399,7	K562	blood:
2	chr1:92197202..92203288-chr1:92206365..92210533,5	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10874911	0.81[ASN][1000 genomes]
rs11165347	0.86[JPT][hapmap]
rs11165377	0.90[CHB][hapmap]
rs11165380	0.83[YRI][hapmap]
rs11165390	0.95[CHB][hapmap];0.91[CHD][hapmap]
rs12066159	0.95[CHB][hapmap];0.91[CHD][hapmap]
rs12123737	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17513917	0.95[CHB][hapmap];0.91[CHD][hapmap]
rs2029356	0.95[CHB][hapmap];0.85[CHD][hapmap]
rs284876	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs4658112	0.95[CHB][hapmap];0.88[CHD][hapmap]
rs6685808	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv2763581	chr1:92068967-92203803	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv1014990	chr1:92084142-92206674	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12076549	ARHGAP29	cis	parietal	SCAN
rs12076549	TGFBR3	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92173200-92202400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:92189200-92202200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:92191800-92204000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:92193000-92202400	Weak transcription	Aorta	Aorta
5	chr1:92197000-92215200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:92197200-92202400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:92197200-92202600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:92197200-92215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:92197600-92203000	Enhancers	Fetal Intestine Small	intestine
10	chr1:92197600-92203400	Enhancers	Fetal Intestine Large	intestine
11	chr1:92197600-92230000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:92197800-92211000	Weak transcription	Colonic Mucosa	Colon
13	chr1:92198000-92210400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:92198200-92202200	Weak transcription	Brain Anterior Caudate	brain
15	chr1:92198200-92202400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:92198200-92202400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:92198200-92202400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:92198200-92202400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:92198200-92202400	Weak transcription	Stomach Mucosa	stomach
20	chr1:92198200-92202600	Weak transcription	Brain Angular Gyrus	brain
21	chr1:92198200-92206600	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:92198200-92224400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:92198400-92201800	Weak transcription	Psoas Muscle	Psoas
24	chr1:92198400-92202000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:92198400-92202000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:92198400-92202000	Weak transcription	HSMM	muscle
27	chr1:92198400-92202400	Weak transcription	Esophagus	oesophagus
28	chr1:92198400-92202600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:92198400-92202600	Weak transcription	Pancreas	Pancrea
30	chr1:92198400-92202600	Weak transcription	Right Atrium	heart
31	chr1:92198400-92202800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr1:92198400-92207000	Weak transcription	Gastric	stomach
33	chr1:92198400-92207400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:92198400-92210400	Weak transcription	HUVEC	blood vessel
35	chr1:92198600-92201800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:92198600-92202200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:92198600-92202200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:92198600-92204400	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr1:92198600-92207600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:92198800-92202000	Weak transcription	HSMMtube	muscle
41	chr1:92198800-92202000	Weak transcription	NH-A	brain
42	chr1:92198800-92202200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:92198800-92203800	Enhancers	Fetal Kidney	kidney
44	chr1:92199000-92201800	Weak transcription	Lung	lung
45	chr1:92199000-92202000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:92199000-92202200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:92199000-92203200	Genic enhancers	K562	blood
48	chr1:92199000-92206200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:92199200-92202200	Weak transcription	Fetal Thymus	thymus
50	chr1:92199200-92202200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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