Variant report

Variant	rs11720139
Chromosome Location	chr3:47036756-47036757
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:47036212-47037360	K562	blood:	n/a	n/a
2	POLR2A	chr3:47036291-47040424	K562	blood:	n/a	n/a
3	POLR2A	chr3:47036515-47037261	GM18505	blood:	n/a	n/a
4	POLR2A	chr3:47035944-47039006	GM12892	blood:	n/a	n/a
5	POLR2A	chr3:47036607-47037224	MCF-7	breast:	n/a	n/a
6	POLR2A	chr3:47036666-47037735	K562	blood:	n/a	n/a
7	POLR2A	chr3:47036236-47038925	K562	blood:	n/a	n/a
8	POLR2A	chr3:47036080-47042185	GM12892	blood:	n/a	n/a
9	POLR2A	chr3:47036630-47037143	GM12891	blood:	n/a	n/a
10	POLR2A	chr3:47036756-47037046	A549	lung:	n/a	n/a
11	POLR2A	chr3:47036354-47038212	A549	lung:	n/a	n/a
12	POLR2A	chr3:47036739-47037080	A549	lung:	n/a	n/a
13	POLR2A	chr3:47036289-47037836	K562	blood:	n/a	n/a
14	POLR2A	chr3:47035079-47040669	K562	blood:	n/a	n/a
15	POLR2A	chr3:47034482-47040584	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:47036396-47039745	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:47036276-47040584	K562	blood:	n/a	n/a
18	POLR2A	chr3:47036329-47040671	HL-60	blood:	n/a	n/a
19	POLR2A	chr3:47036247-47040604	GM12892	blood:	n/a	n/a
20	POLR2A	chr3:47036391-47038903	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47022327..47024798-chr3:47034790..47037154,3	MCF-7	breast:
2	chr3:47029851..47036778-chr3:47036995..47040214,6	MCF-7	breast:

No data

Variant related genes	Relation type
NBEAL2	TF binding region
ENSG00000160799	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10433549	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10461018	0.88[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs1079276	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs1108301	0.88[EUR][1000 genomes]
rs11130110	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11130111	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs11130112	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs11130115	0.92[CEU][hapmap]
rs11707736	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11709660	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11713693	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11714373	0.85[ASN][1000 genomes]
rs11715121	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11716553	0.83[EUR][1000 genomes]
rs11719738	0.86[ASN][1000 genomes]
rs11917361	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11917474	0.87[EUR][1000 genomes]
rs11923706	0.85[ASN][1000 genomes]
rs12152493	0.87[EUR][1000 genomes]
rs12491473	0.85[EUR][1000 genomes]
rs12493425	0.88[ASN][1000 genomes]
rs12630534	0.84[EUR][1000 genomes]
rs12631730	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs12715421	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13061071	0.92[CEU][hapmap]
rs13062681	0.92[EUR][1000 genomes]
rs13066214	0.91[EUR][1000 genomes]
rs13077398	0.87[EUR][1000 genomes]
rs13091054	0.80[EUR][1000 genomes]
rs1463393	0.85[EUR][1000 genomes]
rs17784127	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1811652	0.85[ASN][1000 genomes]
rs1869869	0.87[EUR][1000 genomes]
rs2061197	0.88[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs2278963	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305634	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs2305635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305638	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2385867	0.87[EUR][1000 genomes]
rs34103310	0.82[EUR][1000 genomes]
rs34344887	0.90[EUR][1000 genomes]
rs4018905	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4078466	0.88[CEU][hapmap]
rs4082155	0.88[CEU][hapmap]
rs4234465	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs4682831	0.88[EUR][1000 genomes]
rs4682837	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs4682844	0.88[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4682852	0.93[CEU][hapmap]
rs4683296	0.91[YRI][hapmap]
rs4683297	1.00[YRI][hapmap]
rs4683322	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55724164	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55843455	0.88[EUR][1000 genomes]
rs55927279	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56217494	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56249396	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57756484	0.82[ASN][1000 genomes]
rs58956475	0.83[ASN][1000 genomes]
rs61729713	0.88[EUR][1000 genomes]
rs62246375	0.87[EUR][1000 genomes]
rs62246398	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62246451	0.85[ASN][1000 genomes]
rs62246455	0.81[ASN][1000 genomes]
rs62248439	0.85[EUR][1000 genomes]
rs6414435	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6414436	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6442055	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6442059	0.88[ASN][1000 genomes]
rs66539935	0.88[EUR][1000 genomes]
rs66564457	0.85[EUR][1000 genomes]
rs6763236	0.82[EUR][1000 genomes]
rs6766230	0.86[ASN][1000 genomes]
rs6767218	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6767907	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[ASN][1000 genomes]
rs6768722	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6772670	0.95[CEU][hapmap]
rs6773521	0.82[ASN][1000 genomes]
rs6774733	0.84[EUR][1000 genomes]
rs6777145	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6781941	0.82[ASN][1000 genomes]
rs6791062	0.88[ASN][1000 genomes]
rs6794193	0.81[EUR][1000 genomes]
rs6808742	0.85[EUR][1000 genomes]
rs7373821	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7426969	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7433300	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[ASN][1000 genomes]
rs749511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749512	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610620	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7610636	0.86[EUR][1000 genomes]
rs7617689	0.85[EUR][1000 genomes]
rs7620997	0.85[ASN][1000 genomes]
rs7623888	0.85[ASN][1000 genomes]
rs7625067	0.82[EUR][1000 genomes]
rs7625070	0.82[EUR][1000 genomes]
rs7628747	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs7633435	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7633698	0.87[EUR][1000 genomes]
rs7636252	0.87[EUR][1000 genomes]
rs7640397	0.84[EUR][1000 genomes]
rs7645278	1.00[YRI][hapmap]
rs9311403	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9812878	0.88[ASN][1000 genomes]
rs9818382	0.86[ASN][1000 genomes]
rs9821119	0.85[ASN][1000 genomes]
rs9837343	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[ASN][1000 genomes]
rs9844122	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9845728	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9852082	0.85[YRI][hapmap]
rs9854790	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9858443	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9875235	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	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
7	esv1800172	chr3:47013346-47049306	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv590209	chr3:47018214-47050784	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
9	nsv876757	chr3:47018214-47058057	Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11720139	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs11720139	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47022400-47039800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:47022400-47041600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:47022400-47041800	Weak transcription	Brain Germinal Matrix	brain
4	chr3:47022400-47042000	Weak transcription	Brain Substantia Nigra	brain
5	chr3:47022600-47049000	Weak transcription	Hela-S3	cervix
6	chr3:47022600-47050600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:47023200-47042000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:47024400-47039600	Weak transcription	HepG2	liver
9	chr3:47029400-47038200	Strong transcription	Fetal Stomach	stomach
10	chr3:47029600-47038000	Weak transcription	HMEC	breast
11	chr3:47029800-47038000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:47029800-47038400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:47029800-47039200	Strong transcription	Fetal Intestine Small	intestine
14	chr3:47029800-47040800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:47029800-47040800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:47029800-47041000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:47029800-47042000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:47029800-47042400	Weak transcription	Small Intestine	intestine
19	chr3:47029800-47042600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:47029800-47050600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:47030000-47037800	Strong transcription	Fetal Intestine Large	intestine
22	chr3:47030000-47039400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:47030200-47037400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:47030200-47044600	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:47030400-47038200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:47030400-47039600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:47030800-47045600	Weak transcription	Aorta	Aorta
28	chr3:47031000-47036800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:47031000-47038000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr3:47031000-47039600	Weak transcription	A549	lung
31	chr3:47031000-47040000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr3:47031000-47040400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:47031000-47041800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:47031000-47049600	Strong transcription	Gastric	stomach
35	chr3:47031000-47050200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:47031000-47053000	Strong transcription	Dnd41	blood
37	chr3:47031200-47037400	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr3:47031200-47039800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr3:47031400-47037400	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr3:47031400-47038400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr3:47031400-47039800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr3:47031600-47037200	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:47031600-47038000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:47031600-47038000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:47031600-47039800	Strong transcription	Pancreas	Pancrea
46	chr3:47031800-47043400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:47032000-47041800	Weak transcription	HUVEC	blood vessel
48	chr3:47032000-47042400	Strong transcription	Lung	lung
49	chr3:47032200-47037400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:47032200-47041000	Weak transcription	H9 Cell Line	embryonic stem cell

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