Variant report

Variant	rs3817011
Chromosome Location	chr12:122819566-122819567
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122818073..122820866-chr12:122883137..122886125,2	K562	blood:
2	chr12:122813470..122815000-chr12:122818982..122820696,2	K562	blood:
3	chr12:122819260..122821230-chr12:122903461..122905626,2	K562	blood:
4	chr12:122818766..122820604-chr12:122879832..122881735,2	K562	blood:
5	chr12:122753193..122755127-chr12:122818858..122820589,2	K562	blood:
6	chr12:122818435..122821070-chr12:122965496..122967266,2	K562	blood:
7	chr12:122810184..122811861-chr12:122817902..122819649,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000033030	Chromatin interaction
ENSG00000130779	Chromatin interaction
ENSG00000257097	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10161534	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10734915	0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10734918	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10734924	0.88[JPT][hapmap];0.80[TSI][hapmap]
rs10744208	0.82[EUR][1000 genomes]
rs10744209	0.83[EUR][1000 genomes]
rs10744210	0.84[EUR][1000 genomes]
rs10744211	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs10773075	0.82[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10773088	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773103	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10773104	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10773152	0.84[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs10773167	0.84[EUR][1000 genomes]
rs10773208	0.87[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs10846664	0.84[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10846688	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs10846699	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10846746	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10846764	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10846792	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10846830	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10846921	0.94[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs10846978	0.87[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs10998	0.87[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs11057786	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11057797	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11057882	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11058034	0.83[EUR][1000 genomes]
rs11058226	0.94[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs11058402	0.88[JPT][hapmap]
rs11616082	0.83[EUR][1000 genomes]
rs11836188	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12369858	0.84[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap]
rs12372756	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12581249	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1473553	0.87[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap]
rs1553179	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1803290	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1818050	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1973463	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2062488	0.89[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs2173582	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2341439	0.84[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28730465	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34129612	0.82[EUR][1000 genomes]
rs4039670	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4758643	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4758648	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap]
rs4758662	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4758666	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs4758667	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4997380	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55834409	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6488933	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6488939	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6488951	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6488958	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6489002	0.84[EUR][1000 genomes]
rs7135419	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7294559	0.84[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7301515	0.84[CEU][hapmap];0.91[TSI][hapmap]
rs7314638	0.87[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap]
rs7397299	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7952868	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7953007	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7956480	0.84[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7964138	0.89[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs7969429	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7974262	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7975747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9788145	0.81[EUR][1000 genomes]
rs9988963	0.87[CHD][hapmap];0.88[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3817011	GATC	cis	cerebellum	SCAN
rs3817011	PRKCH	trans	lymphoblastoid	seeQTL
rs3817011	B3GNT4	cis	cerebellum	SCAN
rs3817011	RNF34	cis	parietal	SCAN
rs3817011	NME2P1	cis	cerebellum	SCAN
rs3817011	GTF2H3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122754600-122822400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr12:122770200-122821600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr12:122770400-122821800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:122775600-122833600	Strong transcription	Liver	Liver
5	chr12:122776000-122822200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:122780000-122827200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:122781400-122821400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr12:122785800-122827200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr12:122788200-122821200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:122791200-122841600	Strong transcription	Placenta	Placenta
11	chr12:122792400-122819800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:122794600-122832600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:122797200-122822400	Strong transcription	Fetal Muscle Leg	muscle
14	chr12:122800400-122820600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:122804200-122839000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:122806200-122821400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:122809600-122822000	Strong transcription	Fetal Intestine Small	intestine
18	chr12:122809600-122827400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:122809800-122820600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:122810000-122820800	Strong transcription	Fetal Stomach	stomach
21	chr12:122810000-122820800	Strong transcription	Osteobl	bone
22	chr12:122810000-122821200	Strong transcription	Stomach Smooth Muscle	stomach
23	chr12:122810000-122821400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr12:122810200-122820200	Strong transcription	Right Ventricle	heart
25	chr12:122810200-122820600	Strong transcription	Lung	lung
26	chr12:122810400-122821800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:122810600-122820000	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:122812600-122820600	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr12:122812600-122820600	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr12:122812800-122820800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr12:122812800-122829400	Weak transcription	Fetal Heart	heart
32	chr12:122812800-122839400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:122812800-122839400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:122812800-122844000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr12:122812800-122850600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr12:122813000-122839400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr12:122813400-122820600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:122814400-122820000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr12:122814400-122820600	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr12:122814600-122819600	Strong transcription	Colon Smooth Muscle	Colon
41	chr12:122814600-122819800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:122814600-122820000	Strong transcription	Fetal Intestine Large	intestine
43	chr12:122814600-122820200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr12:122814600-122820600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr12:122814600-122820600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:122814600-122820600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:122814600-122820600	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr12:122814600-122820600	Strong transcription	Rectal Smooth Muscle	rectum
49	chr12:122814600-122820800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:122814800-122820600	Strong transcription	Fetal Thymus	thymus

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