Variant report

Variant	rs9420
Chromosome Location	chr11:57510294-57510295
allele	A/G
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:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:57508432..57511977-chr11:57530270..57533342,3	MCF-7	breast:
2	chr11:57440494..57443306-chr11:57507739..57511429,4	K562	blood:
3	chr11:57507833..57511012-chr11:57515890..57519512,4	MCF-7	breast:
4	chr11:57509911..57512073-chr11:57545879..57548404,2	MCF-7	breast:
5	chr11:57478095..57482223-chr11:57507421..57512003,5	K562	blood:
6	chr11:57508102..57510467-chr11:57518136..57520066,2	MCF-7	breast:
7	chr11:57510237..57513047-chr11:57544366..57548086,3	MCF-7	breast:
8	chr11:57478095..57481312-chr11:57507421..57511942,8	K562	blood:
9	chr11:57416509..57419295-chr11:57509568..57512318,2	K562	blood:
10	chr11:57431371..57436913-chr11:57505728..57511660,10	K562	blood:
11	chr11:57478057..57480948-chr11:57506438..57510938,4	MCF-7	breast:
12	chr11:57193239..57196131-chr11:57510103..57512063,2	K562	blood:
13	chr11:57508686..57513679-chr11:57564628..57569734,7	K562	blood:
14	chr11:57508369..57511140-chr11:57577565..57580322,2	MCF-7	breast:
15	chr11:57510288..57512656-chr11:57528319..57530305,2	K562	blood:
16	chr11:57434290..57436913-chr11:57507221..57510395,5	K562	blood:
17	chr11:57508846..57511581-chr11:57547881..57549731,2	K562	blood:
18	chr11:57104191..57107029-chr11:57508169..57510390,2	MCF-7	breast:
19	chr11:57507427..57512619-chr11:57528805..57534217,7	K562	blood:
20	chr11:57439534..57442360-chr11:57509028..57511429,2	K562	blood:
21	chr11:57478353..57481972-chr11:57506953..57510365,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000156603	Chromatin interaction
ENSG00000134802	Chromatin interaction
ENSG00000213593	Chromatin interaction
ENSG00000254602	Chromatin interaction
ENSG00000198561	Chromatin interaction
ENSG00000254462	Chromatin interaction
ENSG00000233436	Chromatin interaction
ENSG00000109991	Chromatin interaction
ENSG00000166793	Chromatin interaction
ENSG00000156599	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10792112	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896633	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10896636	0.86[CEU][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10896647	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11229066	1.00[JPT][hapmap]
rs11229067	1.00[JPT][hapmap]
rs11229113	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229116	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229130	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229131	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229148	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11570190	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11601320	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11601449	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11602109	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11603020	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs11604325	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11604333	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11605731	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11606396	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11606677	1.00[JPT][hapmap]
rs11607056	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12146541	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12362166	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12785533	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12790196	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12804972	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12805841	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12807250	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1647405	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17455520	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2081361	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2847308	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2926656	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35808061	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3781885	0.89[EUR][1000 genomes]
rs3824988	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs4827	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs488769	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4926	1.00[JPT][hapmap]
rs499188	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs527528	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs543725	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs547891	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576859	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591434	0.80[ASN][1000 genomes]
rs682503	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs708228	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7116341	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7117205	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs7117878	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7121169	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7129727	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71484461	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71484468	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs731384	0.86[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs7932091	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7936998	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7938083	0.93[EUR][1000 genomes]
rs7949841	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	25056061	GWAS catalog

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9420	PRG3	cis	parietal	SCAN
rs9420	MED19	cis	cerebellum	SCAN
rs9420	OR4D10	cis	parietal	SCAN
rs9420	MED19	Cis_1M	lymphoblastoid	RTeQTL
rs9420	MS4A7	cis	parietal	SCAN
rs9420	TIMM10	cis	parietal	SCAN
rs9420	OR5T1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57508200-57510600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:57508400-57510400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:57508400-57510400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr11:57509400-57510400	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr11:57509400-57510400	Flanking Active TSS	Rectal Smooth Muscle	rectum
6	chr11:57509600-57510400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr11:57509600-57510400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
8	chr11:57509600-57510400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr11:57509600-57510400	Flanking Active TSS	Liver	Liver
10	chr11:57509600-57510400	Flanking Active TSS	Brain Angular Gyrus	brain
11	chr11:57509600-57510400	Flanking Active TSS	Brain Hippocampus Middle	brain
12	chr11:57509600-57510400	Flanking Active TSS	Fetal Brain Male	brain
13	chr11:57509600-57510400	Flanking Active TSS	Fetal Stomach	stomach
14	chr11:57509600-57510400	Flanking Active TSS	Right Ventricle	heart
15	chr11:57509600-57510400	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr11:57509600-57510600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:57509600-57510600	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr11:57509600-57510600	Transcr. at gene 5' and 3'	Dnd41	blood
19	chr11:57509800-57510400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr11:57509800-57510400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr11:57509800-57510400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr11:57509800-57510400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr11:57509800-57510400	Flanking Active TSS	Fetal Heart	heart
24	chr11:57509800-57510400	Enhancers	Spleen	Spleen
25	chr11:57509800-57510400	Flanking Active TSS	Hela-S3	cervix
26	chr11:57509800-57510400	Transcr. at gene 5' and 3'	HepG2	liver
27	chr11:57509800-57510400	Flanking Active TSS	HUVEC	blood vessel
28	chr11:57509800-57510400	Transcr. at gene 5' and 3'	K562	blood
29	chr11:57509800-57510400	Flanking Active TSS	NH-A	brain
30	chr11:57509800-57510600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:57509800-57510600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr11:57509800-57510600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
33	chr11:57509800-57510600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr11:57509800-57511200	Weak transcription	Aorta	Aorta
35	chr11:57509800-57519400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr11:57510000-57510400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
37	chr11:57510000-57510400	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr11:57510000-57510400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
39	chr11:57510000-57510400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
40	chr11:57510000-57510400	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
41	chr11:57510000-57510400	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
42	chr11:57510000-57510400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:57510000-57510400	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr11:57510000-57510400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:57510000-57510400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:57510000-57510400	Transcr. at gene 5' and 3'	Brain Anterior Caudate	brain
47	chr11:57510000-57510400	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
48	chr11:57510000-57510400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:57510000-57510400	Enhancers	Esophagus	oesophagus
50	chr11:57510000-57510400	Flanking Active TSS	Fetal Intestine Large	intestine

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