Variant report

Variant	rs4146727
Chromosome Location	chr10:98372104-98372105
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:98366804..98369956-chr10:98370785..98374405,6	K562	blood:
2	chr10:98372033..98373765-chr10:98376062..98378595,2	MCF-7	breast:
3	chr10:98346216..98348806-chr10:98369688..98372310,2	K562	blood:
4	chr10:98367008..98370019-chr10:98371148..98375452,4	K562	blood:
5	chr10:98346216..98350490-chr10:98369688..98376085,7	K562	blood:

Variant related genes	Relation type
ENSG00000155629	Chromatin interaction
ENSG00000077147	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1018604	0.81[ASN][1000 genomes]
rs1018605	0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs1051450	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1063605	0.86[ASN][1000 genomes]
rs10736114	0.82[ASN][1000 genomes]
rs10882809	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs10882811	0.81[CHD][hapmap]
rs10882815	0.81[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs10882821	0.80[ASN][1000 genomes]
rs10882826	0.88[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs10882827	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10882828	0.82[ASN][1000 genomes]
rs11188815	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11188817	0.81[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs11188822	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11188825	0.81[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs11188831	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs11188832	0.83[ASN][1000 genomes]
rs11188833	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs11188840	0.89[ASN][1000 genomes]
rs11188842	0.86[ASN][1000 genomes]
rs11188844	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs11188847	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11188848	0.94[ASN][1000 genomes]
rs11188853	0.90[ASN][1000 genomes]
rs11188854	0.86[ASN][1000 genomes]
rs11188857	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11188858	0.90[ASN][1000 genomes]
rs1132913	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs1132914	1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs12218847	1.00[CHB][hapmap]
rs12219275	1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12220047	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs12414612	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12416646	0.81[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs12775533	1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs12776810	0.86[ASN][1000 genomes]
rs12779720	0.82[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap]
rs1324255	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1324256	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1324259	0.81[ASN][1000 genomes]
rs1324261	0.88[ASN][1000 genomes]
rs1408367	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.83[ASN][1000 genomes]
rs1983831	0.87[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2025451	0.81[ASN][1000 genomes]
rs2031326	0.81[ASW][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs33964467	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.80[ASN][1000 genomes]
rs35779764	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.80[ASN][1000 genomes]
rs36098523	0.94[ASN][1000 genomes]
rs3689	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3748234	0.81[CHD][hapmap]
rs3748235	0.84[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs3748236	0.95[ASN][1000 genomes]
rs3748237	0.86[ASN][1000 genomes]
rs4485036	0.81[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs4534508	0.81[ASW][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs4917742	0.82[ASN][1000 genomes]
rs4919029	0.80[CHD][hapmap]
rs4919037	0.81[ASN][1000 genomes]
rs4919040	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs58305369	0.94[ASN][1000 genomes]
rs61858194	0.92[ASN][1000 genomes]
rs61859300	0.86[ASN][1000 genomes]
rs7069429	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs7070686	0.86[ASN][1000 genomes]
rs7071044	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.86[ASN][1000 genomes]
rs7071224	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7071881	0.86[ASN][1000 genomes]
rs7073017	0.94[ASN][1000 genomes]
rs7073682	0.94[ASN][1000 genomes]
rs7074516	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs7082873	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs7085389	0.86[ASN][1000 genomes]
rs7086213	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs7091606	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs7097291	0.81[ASN][1000 genomes]
rs7101320	0.91[ASN][1000 genomes]
rs713251	0.92[CHD][hapmap]
rs727329	0.81[ASN][1000 genomes]
rs7448	0.81[CHD][hapmap];0.81[ASN][1000 genomes]
rs7478356	0.86[ASN][1000 genomes]
rs8578	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs912480	0.82[CHD][hapmap]
rs927639	0.88[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs9633703	0.81[CHD][hapmap]
rs9664749	0.81[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv895909	chr10:98354924-98382165	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4146727	TBC1D12	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98348000-98373600	Weak transcription	Left Ventricle	heart
2	chr10:98350800-98395600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr10:98352400-98378600	Strong transcription	Liver	Liver
4	chr10:98352400-98399400	Strong transcription	Primary B cells from peripheral blood	blood
5	chr10:98352600-98403000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr10:98353000-98388400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr10:98353000-98403000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr10:98354600-98388600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr10:98357800-98382000	Strong transcription	GM12878-XiMat	blood
10	chr10:98359400-98373400	Weak transcription	Right Ventricle	heart
11	chr10:98360400-98392800	Weak transcription	Thymus	Thymus
12	chr10:98362200-98389200	Strong transcription	Primary B cells from cord blood	blood
13	chr10:98362600-98373600	Weak transcription	Lung	lung
14	chr10:98363800-98392600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr10:98365600-98374200	Enhancers	Fetal Intestine Large	intestine
16	chr10:98365600-98374400	Enhancers	Fetal Intestine Small	intestine
17	chr10:98366000-98388400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr10:98366400-98373400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr10:98366600-98392600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr10:98367200-98372800	Strong transcription	Pancreas	Pancrea
21	chr10:98367200-98375000	Enhancers	Stomach Mucosa	stomach
22	chr10:98367200-98376200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr10:98367400-98375000	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr10:98367400-98376200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr10:98367400-98418600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr10:98368400-98373600	Weak transcription	HSMM	muscle
27	chr10:98368800-98377800	Weak transcription	Brain Anterior Caudate	brain
28	chr10:98369000-98373400	Weak transcription	HSMMtube	muscle
29	chr10:98369200-98372600	Enhancers	HepG2	liver
30	chr10:98370000-98373600	Weak transcription	Gastric	stomach
31	chr10:98370600-98372200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr10:98370600-98375800	Weak transcription	Ovary	ovary
33	chr10:98370800-98373600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr10:98370800-98378600	Weak transcription	Brain Substantia Nigra	brain
35	chr10:98371000-98378800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr10:98371000-98382600	Strong transcription	Spleen	Spleen
37	chr10:98371000-98388600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr10:98371000-98389000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr10:98371200-98372400	Enhancers	Duodenum Mucosa	Duodenum
40	chr10:98371200-98373200	Weak transcription	Placenta	Placenta
41	chr10:98371200-98373200	Weak transcription	K562	blood
42	chr10:98371200-98373600	Weak transcription	Small Intestine	intestine
43	chr10:98371200-98375000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr10:98371800-98372600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr10:98371800-98372600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr10:98371800-98372600	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr10:98371800-98378600	Weak transcription	Colonic Mucosa	Colon
48	chr10:98372000-98372600	Genic enhancers	Rectal Mucosa Donor 29	rectum

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