Variant report

Variant	rs319695
Chromosome Location	chr3:47884239-47884240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:47884175-47884344	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:47884091-47884478	K562	blood:	n/a	n/a
3	POLR2A	chr3:47884124-47886762	K562	blood:	n/a	n/a
4	POLR2A	chr3:47884152-47886806	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:47884204-47884245	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:47884173-47886804	U87	brain:	n/a	n/a
7	POLR2A	chr3:47884159-47886667	K562	blood:	n/a	n/a
8	POLR2A	chr3:47884213-47884775	HL-60	blood:	n/a	n/a
9	POLR2A	chr3:47884214-47884537	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:47884079-47884652	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr3:47884204-47884480	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:47884158-47886755	GM12892	blood:	n/a	n/a
13	POLR2A	chr3:47884126-47885319	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:47878857..47881081-chr3:47884231..47886531,2	MCF-7	breast:
2	chr3:47881404..47884302-chr3:47904180..47905829,2	K562	blood:
3	chr3:47881026..47886569-chr3:47887107..47891221,7	K562	blood:
4	chr3:47883704..47886519-chr3:47887947..47890824,2	MCF-7	breast:

No data

Variant related genes	Relation type
DHX30	TF binding region
ENSG00000132153	Chromatin interaction
ENSG00000221585	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1013431	0.83[CHB][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs1060407	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs1061003	0.85[ASN][1000 genomes]
rs11130146	0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs11130148	0.83[ASW][hapmap];0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs11130150	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130152	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs1137524	0.80[ASN][1000 genomes]
rs11707679	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs11710199	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11712464	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs12495204	0.85[CEU][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs12635438	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs13061412	0.91[CEU][hapmap]
rs13063042	0.89[CEU][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs13074973	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs13077230	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13079407	0.91[CEU][hapmap]
rs13091913	0.83[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs13093830	0.91[ASN][1000 genomes]
rs13094264	0.83[ASW][hapmap];0.88[CEU][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs1486915	0.83[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs1684942	0.83[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs17079785	0.89[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs17290490	0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2047559	0.89[CEU][hapmap]
rs2121754	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs2133601	0.82[CEU][hapmap];0.86[CHD][hapmap]
rs2140335	0.88[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs2166770	0.83[CHB][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs2351248	0.88[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs2631721	0.84[ASN][1000 genomes]
rs2882611	0.88[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap]
rs319681	0.93[ASN][1000 genomes]
rs319682	0.83[CHB][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs319684	0.80[ASN][1000 genomes]
rs319685	0.80[ASN][1000 genomes]
rs319686	0.80[ASN][1000 genomes]
rs319689	0.80[ASN][1000 genomes]
rs319692	0.82[ASN][1000 genomes]
rs319693	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319694	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs319696	0.83[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs34025851	0.80[ASN][1000 genomes]
rs34249203	0.81[EUR][1000 genomes]
rs34750113	0.88[ASN][1000 genomes]
rs35199727	0.91[ASN][1000 genomes]
rs35314534	0.82[ASN][1000 genomes]
rs35582375	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3732529	0.80[ASN][1000 genomes]
rs3772399	0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3888	0.83[ASW][hapmap];0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3915654	0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4599334	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs4858846	0.92[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap]
rs4858851	0.83[ASW][hapmap];0.89[CEU][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs4858860	0.83[ASW][hapmap];0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858863	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858871	0.83[CHB][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs60446735	0.80[ASN][1000 genomes]
rs62263575	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6442082	0.88[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs6442091	0.81[ASN][1000 genomes]
rs6768699	0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs6772301	0.88[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs6772396	0.80[ASN][1000 genomes]
rs6776963	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.82[ASN][1000 genomes]
rs6777632	0.88[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs6785669	0.83[ASW][hapmap];0.88[CEU][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs6786001	0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs6792497	0.89[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs6806860	0.84[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs7374516	0.83[CHB][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs7426976	0.83[CHB][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap]
rs7427418	0.83[CHB][hapmap]
rs7429162	0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs7430879	0.83[CHB][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs7430913	0.93[JPT][hapmap]
rs7618758	0.89[CEU][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs7621236	0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs7624474	0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs7629850	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7638103	0.83[ASW][hapmap];0.89[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs7645846	0.90[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs777015	0.83[CHB][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs777017	0.93[ASN][1000 genomes]
rs796566	0.80[ASN][1000 genomes]
rs800762	0.82[ASN][1000 genomes]
rs810334	0.83[CHB][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs9681917	0.83[ASW][hapmap];0.89[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs9850154	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9862913	0.83[CHB][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834679	chr3:47749475-47924006	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
2	nsv1006560	chr3:47867461-48037031	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	141 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs319695	ZNF589	cis	Nerve Tibial	GTEx
rs319695	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs319695	SMARCC1	cis	cerebellum	SCAN
rs319695	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs319695	ZNF589	cis	cerebellum	SCAN
rs319695	NME6	cis	Esophagus Muscularis	GTEx
rs319695	HYAL2	cis	cerebellum	SCAN
rs319695	MRPS18AP1	cis	Nerve Tibial	GTEx
rs319695	ZNF589	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47867800-47899200	Strong transcription	Fetal Brain Female	brain
2	chr3:47867800-47918800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:47868000-47903000	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:47868000-47915200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:47868200-47892200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:47868200-47902400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr3:47868400-47884400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:47868400-47891000	Strong transcription	Fetal Muscle Leg	muscle
9	chr3:47868400-47891200	Strong transcription	Fetal Muscle Trunk	muscle
10	chr3:47868400-47891400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:47868400-47899200	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr3:47868400-47901200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:47868400-47902400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:47868400-47903000	Strong transcription	Placenta	Placenta
15	chr3:47868400-47903400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:47868400-47903400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:47868400-47916400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:47868400-47919000	Strong transcription	Fetal Stomach	stomach
19	chr3:47868600-47893600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:47868600-47899000	Strong transcription	Thymus	Thymus
21	chr3:47868600-47899200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr3:47868600-47899200	Strong transcription	Primary T cells from cord blood	blood
23	chr3:47868600-47899400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:47868600-47901800	Strong transcription	Fetal Intestine Large	intestine
25	chr3:47868600-47902200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr3:47868600-47902600	Strong transcription	Liver	Liver
27	chr3:47868600-47902800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:47868600-47912200	Strong transcription	Fetal Intestine Small	intestine
29	chr3:47868800-47890400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:47868800-47894000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:47868800-47902000	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:47868800-47902200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr3:47868800-47902400	Strong transcription	Osteobl	bone
34	chr3:47869000-47897400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:47869000-47897400	Strong transcription	Adipose Nuclei	Adipose
36	chr3:47869000-47897800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:47869000-47899400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:47869000-47902400	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:47869000-47918600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:47869200-47902200	Strong transcription	Dnd41	blood
41	chr3:47870800-47931800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr3:47871200-47899200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:47871400-47892600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:47871400-47899200	Strong transcription	Fetal Thymus	thymus
45	chr3:47871600-47892000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:47871600-47894200	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:47871600-47899200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:47871800-47899200	Strong transcription	Gastric	stomach
49	chr3:47871800-47901600	Strong transcription	Brain Germinal Matrix	brain
50	chr3:47872000-47899400	Strong transcription	Primary T helper cells fromperipheralblood	blood

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