Variant report

Variant	rs2932539
Chromosome Location	chr1:113215786-113215787
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:113215591-113217660	SK-N-SH	brain:	n/a	n/a
2	NFATC1	chr1:113215756-113217662	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:113214019-113219584	K562	blood:	n/a	n/a
4	BCLAF1	chr1:113215699-113217809	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:113215444-113217912	U87	brain:	n/a	n/a
6	POLR2A	chr1:113214953-113217727	GM12891	blood:	n/a	n/a
7	POLR2A	chr1:113215547-113218210	K562	blood:	n/a	n/a
8	TEAD4	chr1:113215431-113219568	K562	blood:	n/a	n/a
9	POLR2A	chr1:113214734-113217689	GM12892	blood:	n/a	n/a
10	POLR2A	chr1:113215428-113217721	GM12892	blood:	n/a	n/a
11	POLR2A	chr1:113215582-113218541	K562	blood:	n/a	n/a
12	POLR2A	chr1:113215775-113215796	HepG2	liver:	n/a	n/a
13	POLR2A	chr1:113215438-113217912	U87	brain:	n/a	n/a
14	POLR2A	chr1:113215459-113218377	GM12878	blood:	n/a	n/a
15	TEAD4	chr1:113215588-113217476	K562	blood:	n/a	n/a
16	POLR2A	chr1:113215573-113216157	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr1:113215529-113215874	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr1:113215124-113218356	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr1:113215417-113218255	GM12892	blood:	n/a	n/a
20	POLR2A	chr1:113215470-113217762	GM12891	blood:	n/a	n/a
21	PML	chr1:113215352-113218256	K562	blood:	n/a	n/a
22	POLR2A	chr1:113215407-113215808	PFSK-1	brain:	n/a	n/a
23	CTCF	chr1:113215760-113215910	HPAF	blood vessel:	n/a	n/a
24	POLR2A	chr1:113214902-113217806	HL-60	blood:	n/a	n/a
25	POLR2A	chr1:113214234-113217824	GM12892	blood:	n/a	n/a
26	PML	chr1:113215169-113218208	K562	blood:	n/a	n/a
27	POLR2A	chr1:113215735-113218268	GM18505	blood:	n/a	n/a
28	POLR2A	chr1:113215395-113218531	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr1:113215198-113217637	GM12891	blood:	n/a	n/a
30	POLR2A	chr1:113215648-113215818	GM12891	blood:	n/a	n/a
31	POLR2A	chr1:113214919-113218137	K562	blood:	n/a	n/a
32	POLR2A	chr1:113215571-113218049	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:113214882-113218215	GM12878	blood:	n/a	n/a
34	POLR2A	chr1:113215505-113218188	K562	blood:	n/a	n/a
35	POLR2A	chr1:113215375-113218243	HUVEC	blood vessel:	n/a	n/a
36	MTA3	chr1:113215605-113217858	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:113215685-113218282	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr1:113215448-113217677	PANC-1	pancreas:	n/a	n/a
39	POLR2A	chr1:113215419-113218438	K562	blood:	n/a	n/a
40	POLR2A	chr1:113215302-113216016	K562	blood:	n/a	n/a
41	POLR2A	chr1:113214937-113218306	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr1:113215321-113217934	K562	blood:	n/a	n/a
43	POLR2A	chr1:113214892-113217760	A549	lung:	n/a	n/a
44	POLR2A	chr1:113214365-113217673	HepG2	liver:	n/a	n/a
45	POLR2A	chr1:113214802-113218719	K562	blood:	n/a	n/a
46	POLR2A	chr1:113215411-113217936	GM12891	blood:	n/a	n/a
47	NFATC1	chr1:113215707-113217704	GM12878	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113201056..113203899-chr1:113214909..113217826,3	MCF-7	breast:
2	chr1:113215712..113221627-chr1:113253708..113259381,5	MCF-7	breast:
3	chr1:113158395..113164969-chr1:113214433..113222934,24	MCF-7	breast:
4	chr1:113215224..113219998-chr1:113238829..113244717,20	MCF-7	breast:
5	chr1:113214782..113217536-chr1:113235013..113236894,2	K562	blood:
6	chr1:113160799..113166409-chr1:113215716..113220433,9	K562	blood:
7	chr1:113214002..113222947-chr1:113236890..113251579,47	MCF-7	breast:
8	chr1:113208980..113212025-chr1:113215390..113218147,4	MCF-7	breast:
9	chr1:113214590..113222957-chr1:113244863..113253590,39	MCF-7	breast:
10	chr1:113157097..113164348-chr1:113214570..113220795,12	MCF-7	breast:
11	chr1:113214866..113222565-chr1:113237012..113253952,54	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MOV10-1	chr1:113215763-113216073	NONHSAT005272

No data

Variant related genes	Relation type
MOV10	TF binding region
ENSG00000155363	Chromatin interaction
ENSG00000261595	Chromatin interaction
ENSG00000155366	Chromatin interaction
ENSG00000225075	Chromatin interaction
ENSG00000155367	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000271810	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10745331	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs10745332	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10857969	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11102508	0.86[ASN][1000 genomes]
rs11102510	0.83[EUR][1000 genomes]
rs11102517	0.80[EUR][1000 genomes]
rs12048528	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12118370	0.85[ASN][1000 genomes]
rs12119489	0.86[ASN][1000 genomes]
rs12125361	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12126494	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12137107	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12138335	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12143068	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1238	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12401734	1.00[CEU][hapmap]
rs12402469	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12402929	0.93[CEU][hapmap]
rs12406906	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12739994	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12750023	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12750621	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12758377	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17438324	0.84[ASN][1000 genomes]
rs2273369	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2932529	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2932534	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2932535	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2932538	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3013433	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3013441	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34531155	0.82[EUR][1000 genomes]
rs35482634	0.84[ASN][1000 genomes]
rs3762335	0.84[ASN][1000 genomes]
rs3790611	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs3790612	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs3795820	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4240534	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4838960	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4838961	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4839257	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61818800	0.89[ASN][1000 genomes]
rs6537740	1.00[CEU][hapmap]
rs6537742	0.83[CEU][hapmap]
rs6537744	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6537745	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6537746	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6537747	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6658555	1.00[CEU][hapmap]
rs6663922	0.82[ASN][1000 genomes]
rs6668533	1.00[CEU][hapmap]
rs6671645	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6673930	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6674053	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6674068	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6681371	1.00[CEU][hapmap]
rs6682678	0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6690169	0.86[ASN][1000 genomes]
rs6690292	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6691025	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6691917	0.86[ASN][1000 genomes]
rs6693880	0.84[ASN][1000 genomes]
rs6696991	0.81[ASN][1000 genomes]
rs6698030	0.82[EUR][1000 genomes]
rs6701351	0.86[ASN][1000 genomes]
rs7415988	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7512984	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7516421	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7522110	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7527076	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7535636	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[ASN][1000 genomes]
rs7542820	0.86[ASN][1000 genomes]
rs7546203	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7551933	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs9429694	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9662162	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs999923	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
5	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2932539	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs2932539	ST7L	cis	lung	GTEx
rs2932539	ST7L	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113168800-113215800	Weak transcription	Fetal Heart	heart
2	chr1:113180000-113216000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:113185400-113216200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:113187800-113216000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:113189800-113216200	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:113194400-113216000	Weak transcription	Stomach Mucosa	stomach
7	chr1:113203400-113216200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:113204200-113216200	Weak transcription	Pancreas	Pancrea
9	chr1:113204200-113216600	Weak transcription	Esophagus	oesophagus
10	chr1:113204200-113216800	Weak transcription	Aorta	Aorta
11	chr1:113204800-113216600	Weak transcription	Small Intestine	intestine
12	chr1:113205000-113216600	Weak transcription	Right Ventricle	heart
13	chr1:113205400-113217000	Weak transcription	Gastric	stomach
14	chr1:113206000-113215800	Strong transcription	HMEC	breast
15	chr1:113206800-113216200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:113207000-113216200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:113208400-113215800	Weak transcription	A549	lung
18	chr1:113208800-113216200	Weak transcription	Brain Angular Gyrus	brain
19	chr1:113208800-113217000	Weak transcription	Spleen	Spleen
20	chr1:113210800-113216600	Weak transcription	Ovary	ovary
21	chr1:113211000-113215800	Weak transcription	Fetal Intestine Small	intestine
22	chr1:113211400-113215800	Strong transcription	Primary B cells from cord blood	blood
23	chr1:113211400-113216200	Weak transcription	Fetal Stomach	stomach
24	chr1:113211400-113216800	Weak transcription	Lung	lung
25	chr1:113212600-113216000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:113212600-113216200	Weak transcription	Fetal Lung	lung
27	chr1:113212600-113216600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:113212600-113216800	Weak transcription	Brain Germinal Matrix	brain
29	chr1:113212800-113215800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:113212800-113215800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:113212800-113216000	Weak transcription	Brain Substantia Nigra	brain
32	chr1:113212800-113216200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:113212800-113216400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr1:113212800-113216800	Weak transcription	Psoas Muscle	Psoas
35	chr1:113213000-113216000	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:113213000-113216200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:113213200-113216000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:113213200-113216200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:113213400-113216000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:113213400-113216200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:113213400-113216200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:113213400-113216200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:113213600-113215800	Weak transcription	Primary T cells from cord blood	blood
44	chr1:113213600-113216200	Weak transcription	Colonic Mucosa	Colon
45	chr1:113213800-113215800	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr1:113213800-113216400	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr1:113213800-113216600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:113214000-113216200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:113214000-113216200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:113214000-113216800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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