Variant report

Variant	rs7977613
Chromosome Location	chr12:48079507-48079508
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48079504..48082471-chr12:48085134..48087838,3	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10783212	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875677	0.99[ASN][1000 genomes]
rs10875682	0.97[ASN][1000 genomes]
rs10875685	0.89[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs10875686	0.83[ASN][1000 genomes]
rs10875687	0.94[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs10875688	0.81[ASN][1000 genomes]
rs11168191	1.00[ASN][1000 genomes]
rs11168192	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[ASN][1000 genomes]
rs11168193	1.00[ASN][1000 genomes]
rs11168199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11168200	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs11168203	0.97[ASN][1000 genomes]
rs11168208	0.94[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs11168214	0.81[ASN][1000 genomes]
rs11168215	0.94[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs11168216	0.81[ASN][1000 genomes]
rs12366410	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs12367193	0.97[ASN][1000 genomes]
rs12370643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1541384	0.97[ASN][1000 genomes]
rs2072117	0.81[ASN][1000 genomes]
rs2240079	0.94[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2240080	0.94[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2283346	0.94[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs3764013	0.94[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]
rs56240307	0.92[ASN][1000 genomes]
rs582680	0.92[ASN][1000 genomes]
rs602143	0.93[ASN][1000 genomes]
rs612773	0.93[ASN][1000 genomes]
rs61917590	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61917591	0.94[ASN][1000 genomes]
rs61917594	0.99[ASN][1000 genomes]
rs61917595	0.98[ASN][1000 genomes]
rs61917616	0.81[ASN][1000 genomes]
rs61917617	0.81[ASN][1000 genomes]
rs630777	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs632944	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs646223	0.92[ASN][1000 genomes]
rs6580634	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs671961	0.93[ASN][1000 genomes]
rs7136561	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs7137529	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7311663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7484827	0.94[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7954502	0.94[ASN][1000 genomes]
rs7969186	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7976748	0.94[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs948393	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430507	chr12:47883933-48079507	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1050043	chr12:47949004-48087218	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv899058	chr12:48012390-48082482	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv695	chr12:48043261-48088221	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7977613	HDAC7	cis	cerebellum	SCAN
rs7977613	RAPGEF3	cis	parietal	SCAN
rs7977613	DDX23	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48029800-48098800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:48031000-48083200	Weak transcription	Esophagus	oesophagus
3	chr12:48040600-48086000	Weak transcription	Fetal Brain Male	brain
4	chr12:48043400-48080000	Weak transcription	NHEK	skin
5	chr12:48046600-48083000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:48046600-48087800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:48046600-48090000	Weak transcription	Psoas Muscle	Psoas
8	chr12:48046600-48097000	Weak transcription	Brain Angular Gyrus	brain
9	chr12:48046600-48097600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:48046600-48099200	Weak transcription	Gastric	stomach
11	chr12:48046800-48083200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:48046800-48098600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr12:48046800-48099000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:48050200-48098600	Weak transcription	Pancreas	Pancrea
15	chr12:48052000-48094400	Weak transcription	Aorta	Aorta
16	chr12:48055200-48083200	Weak transcription	Brain Germinal Matrix	brain
17	chr12:48056000-48099000	Weak transcription	Right Ventricle	heart
18	chr12:48057200-48098800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:48058000-48098600	Weak transcription	Colonic Mucosa	Colon
20	chr12:48058200-48086000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:48058600-48082600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:48058800-48086000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:48059800-48083000	Weak transcription	Fetal Intestine Small	intestine
24	chr12:48059800-48083200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:48060400-48083000	Weak transcription	Spleen	Spleen
26	chr12:48060400-48088400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:48060600-48083000	Weak transcription	Fetal Stomach	stomach
28	chr12:48060600-48084200	Weak transcription	Thymus	Thymus
29	chr12:48060600-48086000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:48060600-48094200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:48060800-48094200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr12:48061600-48088600	Weak transcription	Brain Substantia Nigra	brain
33	chr12:48062000-48083200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:48062600-48094200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr12:48062800-48098600	Weak transcription	Colon Smooth Muscle	Colon
36	chr12:48063000-48086400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr12:48063000-48099000	Weak transcription	Small Intestine	intestine
38	chr12:48064600-48086000	Weak transcription	Lung	lung
39	chr12:48064600-48086000	Weak transcription	HSMMtube	muscle
40	chr12:48064600-48099200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:48064800-48089600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:48064800-48090000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr12:48065000-48092800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr12:48066400-48086000	Weak transcription	Fetal Heart	heart
45	chr12:48068400-48083200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:48068400-48097200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr12:48071200-48080200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:48071800-48091600	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:48072600-48081000	Strong transcription	Primary B cells from peripheral blood	blood
50	chr12:48072800-48086000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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