Variant report

Variant	rs11709525
Chromosome Location	chr3:49690496-49690497
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	chr3:49689149..49690759-chr3:49696566..49699118,2	MCF-7	breast:
2	chr3:49690148..49693099-chr3:49693648..49695606,2	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1050088	0.86[JPT][hapmap]
rs1060962	0.92[CHD][hapmap];0.85[GIH][hapmap];0.81[ASN][1000 genomes]
rs10865955	0.86[JPT][hapmap]
rs11130199	0.86[JPT][hapmap]
rs11130212	0.97[ASN][1000 genomes]
rs11130213	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1131095	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11710037	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711485	0.95[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap]
rs11718165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11720264	0.86[JPT][hapmap]
rs11720597	0.80[AMR][1000 genomes]
rs11917431	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11919311	0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11921590	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12489092	0.86[JPT][hapmap]
rs13064576	0.84[AMR][1000 genomes]
rs13085791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13316695	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352890	0.92[ASN][1000 genomes]
rs1568661	0.86[JPT][hapmap]
rs1801143	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap]
rs1873625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1873626	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2005557	0.81[ASN][1000 genomes]
rs2131104	0.92[CHD][hapmap];0.85[GIH][hapmap];0.81[ASN][1000 genomes]
rs2131109	0.92[CHD][hapmap];0.85[GIH][hapmap]
rs2172252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329020	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2960548	0.87[ASN][1000 genomes]
rs3197999	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34762726	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35007338	0.92[ASN][1000 genomes]
rs35404120	0.92[ASN][1000 genomes]
rs35701831	0.86[JPT][hapmap]
rs3811697	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap]
rs3870338	0.86[JPT][hapmap]
rs3924462	0.86[JPT][hapmap]
rs4283605	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap]
rs4855839	0.86[JPT][hapmap]
rs4855847	0.92[ASN][1000 genomes]
rs4855852	0.92[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4855859	0.86[JPT][hapmap]
rs4855864	0.86[JPT][hapmap]
rs4855881	0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4855884	1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.81[ASN][1000 genomes]
rs6765869	0.81[ASN][1000 genomes]
rs6766131	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap]
rs6770670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803222	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7614725	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7622302	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs7633271	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs7637999	0.86[JPT][hapmap]
rs885592	0.86[JPT][hapmap]
rs9811982	1.00[CEU][hapmap]
rs9812791	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822268	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9823546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9824092	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827021	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9827708	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9833611	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9836291	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9837027	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap]
rs9837341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9837520	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9841110	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9853683	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs9858213	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap]
rs9858280	1.00[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap]
rs9858542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9862080	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875617	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes]
rs9882740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1011428	chr3:49649989-49706068	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11709525	RNF123	cis	cerebellum	SCAN
rs11709525	GPX1	cis	parietal	SCAN
rs11709525	PARP3	cis	parietal	SCAN
rs11709525	CELSR3	cis	cerebellum	SCAN
rs11709525	CISH	cis	lymphoblastoid	seeQTL
rs11709525	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs11709525	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs11709525	RBM6	cis	cerebellum	SCAN
rs11709525	IP6K2	cis	cerebellum	SCAN
rs11709525	ZNF589	cis	parietal	SCAN
rs11709525	RNF123	cis	parietal	SCAN
rs11709525	MYL3	cis	parietal	SCAN
rs11709525	FAM212A	cis	Muscle Skeletal	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49661600-49692400	Weak transcription	Ovary	ovary
2	chr3:49669400-49692000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:49673800-49692400	Weak transcription	Gastric	stomach
4	chr3:49676200-49692000	Weak transcription	Esophagus	oesophagus
5	chr3:49685200-49708200	Strong transcription	Brain Germinal Matrix	brain
6	chr3:49685400-49708400	Strong transcription	Fetal Brain Female	brain
7	chr3:49685600-49693200	Weak transcription	Liver	Liver
8	chr3:49685800-49692600	Weak transcription	Fetal Intestine Small	intestine
9	chr3:49686000-49692400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:49686000-49692600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:49686600-49697200	Weak transcription	Pancreas	Pancrea
12	chr3:49686600-49710600	Weak transcription	Right Atrium	heart
13	chr3:49687000-49695600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:49687600-49691600	Weak transcription	Spleen	Spleen
15	chr3:49687600-49694200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:49687600-49702400	Weak transcription	Right Ventricle	heart
17	chr3:49687600-49705800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:49687800-49691800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:49687800-49694200	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr3:49688000-49695800	Weak transcription	HepG2	liver
21	chr3:49688200-49691000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:49688400-49692000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:49688400-49692400	Strong transcription	Brain Anterior Caudate	brain
24	chr3:49688400-49692400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:49688400-49694000	Strong transcription	Brain Hippocampus Middle	brain
26	chr3:49688600-49692200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:49688800-49691600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:49689000-49692000	Strong transcription	Brain Angular Gyrus	brain
29	chr3:49689000-49693400	Strong transcription	Brain Cingulate Gyrus	brain
30	chr3:49690200-49690600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:49690200-49691000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:49690200-49691800	Enhancers	Fetal Muscle Trunk	muscle
33	chr3:49690200-49692600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr3:49690200-49693400	Weak transcription	Fetal Stomach	stomach
35	chr3:49690400-49696600	Enhancers	Fetal Muscle Leg	muscle
36	chr3:49690400-49702000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:49690400-49710600	Weak transcription	Brain Substantia Nigra	brain

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