Variant report

Variant	rs11710322
Chromosome Location	chr3:47331136-47331137
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	chr3:47330452..47333849-chr3:47334869..47338744,4	MCF-7	breast:
2	chr3:47321748..47325634-chr3:47331051..47333243,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000088727	Chromatin interaction
ENSG00000114648	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1038394	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs1076394	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10865946	0.96[CEU][hapmap]
rs11130115	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs11130123	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130124	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11130126	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes]
rs11130128	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs11130129	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs11705957	0.96[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs11710013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11710121	0.92[ASW][hapmap];0.85[CEU][hapmap];0.84[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11711824	0.96[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs11712445	0.96[CEU][hapmap]
rs11714294	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11716763	0.96[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap]
rs11719877	0.96[CEU][hapmap];0.80[GIH][hapmap];0.93[TSI][hapmap]
rs11915074	0.92[CEU][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes]
rs11920853	0.92[CEU][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes]
rs11921117	0.85[EUR][1000 genomes]
rs12636851	0.96[CEU][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs13061071	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs13072802	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13075233	0.96[CEU][hapmap];0.80[GIH][hapmap];0.93[TSI][hapmap]
rs13094438	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1466741	0.83[YRI][hapmap]
rs1531875	0.96[CEU][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs1638676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17080872	0.81[JPT][hapmap]
rs17410853	0.85[CEU][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap]
rs17411375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs17476234	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872164	0.96[CEU][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs2101247	0.92[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs2132173	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap]
rs2159400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap]
rs2276853	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2276854	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs295428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.80[ASN][1000 genomes]
rs295441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs295458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs295461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs3736177	0.96[CEU][hapmap]
rs4682852	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4683326	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858811	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs4858824	0.96[CEU][hapmap]
rs4858868	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs4858893	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs4858894	0.87[CEU][hapmap];0.88[JPT][hapmap]
rs59689369	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6767907	1.00[ASW][hapmap];0.81[CEU][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap]
rs6768221	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs6772670	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs6780013	0.89[CEU][hapmap];0.89[TSI][hapmap]
rs6791842	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6792461	0.96[CEU][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs6800271	0.96[CEU][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs7636423	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7651762	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs807932	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs807935	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs807936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs807937	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs811115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs878659	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs922957	0.96[CEU][hapmap]
rs9311403	0.84[CEU][hapmap];0.86[YRI][hapmap]
rs9683033	0.96[CEU][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs9837343	1.00[ASW][hapmap];0.81[CEU][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11710322	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs11710322	HYAL2	cis	cerebellum	SCAN
rs11710322	CCDC12	cis	cerebellum	SCAN
rs11710322	NCKIPSD	cis	cerebellum	SCAN
rs11710322	SCAP	cis	parietal	SCAN
rs11710322	PRKAR2A	cis	cerebellum	SCAN
rs11710322	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs11710322	C3orf75	cis	cerebellum	SCAN
rs11710322	AMIGO3	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47325400-47361000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:47325600-47331200	Weak transcription	Aorta	Aorta
3	chr3:47325600-47332000	Weak transcription	Esophagus	oesophagus
4	chr3:47325600-47334200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:47325600-47334400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:47325600-47334400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:47325600-47337800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:47325600-47338000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:47325600-47344600	Weak transcription	Ovary	ovary
10	chr3:47325600-47367600	Weak transcription	A549	lung
11	chr3:47325800-47331400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:47325800-47331600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:47325800-47332400	Weak transcription	Right Ventricle	heart
14	chr3:47325800-47332400	Weak transcription	NH-A	brain
15	chr3:47325800-47337600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:47325800-47338000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:47325800-47338200	Weak transcription	HUVEC	blood vessel
18	chr3:47325800-47343800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:47325800-47352000	Weak transcription	Fetal Kidney	kidney
20	chr3:47326200-47336400	Weak transcription	Lung	lung
21	chr3:47326200-47340800	Weak transcription	Fetal Intestine Large	intestine
22	chr3:47326200-47344600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:47326200-47356200	Weak transcription	Fetal Heart	heart
24	chr3:47326200-47356600	Weak transcription	NHDF-Ad	bronchial
25	chr3:47326200-47359600	Weak transcription	Fetal Lung	lung
26	chr3:47326200-47362200	Weak transcription	Gastric	stomach
27	chr3:47326200-47363200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:47326400-47338200	Weak transcription	Stomach Mucosa	stomach
29	chr3:47326400-47364400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:47326600-47334200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:47326600-47341200	Weak transcription	Placenta	Placenta
32	chr3:47326600-47351600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:47326800-47333600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:47326800-47356600	Weak transcription	Small Intestine	intestine
35	chr3:47327000-47332400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:47327000-47344400	Weak transcription	Brain Angular Gyrus	brain
37	chr3:47327200-47336600	Strong transcription	Primary T cells from cord blood	blood
38	chr3:47327600-47333200	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:47327600-47333600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr3:47327600-47334400	Strong transcription	Fetal Muscle Leg	muscle
41	chr3:47327600-47348400	Weak transcription	Fetal Brain Male	brain
42	chr3:47328000-47331200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:47328000-47332600	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:47328200-47331200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:47328200-47331200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr3:47328200-47331400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:47328200-47332600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:47328200-47332800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:47328200-47333400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr3:47328200-47333800	Strong transcription	Primary T cells fromperipheralblood	blood

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