Variant report

Variant	rs2306940
Chromosome Location	chr1:113241052-113241053
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:44)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:44 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:113240102-113248907	U87	brain:	n/a	n/a
2	POLR2A	chr1:113240693-113241711	GM12878	blood:	n/a	n/a
3	ELF1	chr1:113240867-113241749	K562	blood:	n/a	n/a
4	POLR2A	chr1:113240926-113241693	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:113240738-113245862	K562	blood:	n/a	n/a
6	POLR2A	chr1:113240207-113248892	K562	blood:	n/a	n/a
7	NFIC	chr1:113240994-113241540	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr1:113240458-113241069	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:113240680-113249021	K562	blood:	n/a	n/a
10	MYBL2	chr1:113241046-113241783	HepG2	liver:	n/a	n/a
11	FOSL2	chr1:113241000-113241879	HepG2	liver:	n/a	n/a
12	POLR2A	chr1:113241020-113241789	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:113240211-113248533	A549	lung:	n/a	n/a
14	POLR2A	chr1:113240649-113246839	K562	blood:	n/a	n/a
15	EP300	chr1:113241044-113241935	HepG2	liver:	n/a	n/a
16	BRCA1	chr1:113240996-113241200	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:113240403-113244696	HUVEC	blood vessel:	n/a	n/a
18	RCOR1	chr1:113241018-113241998	K562	blood:	n/a	n/a
19	POLR2A	chr1:113240166-113244996	HUVEC	blood vessel:	n/a	n/a
20	GABPA	chr1:113241026-113241411	K562	blood:	n/a	n/a
21	POLR2A	chr1:113241038-113244807	K562	blood:	n/a	n/a
22	POLR2A	chr1:113240732-113241475	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr1:113240885-113246230	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr1:113241017-113241129	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr1:113240375-113248999	K562	blood:	n/a	n/a
26	JUN	chr1:113240870-113245032	K562	blood:	n/a	chr1:113243606-113243619
27	MAZ	chr1:113240950-113242039	K562	blood:	n/a	n/a
28	TEAD4	chr1:113241031-113244470	K562	blood:	n/a	n/a
29	MXI1	chr1:113240817-113242010	HepG2	liver:	n/a	n/a
30	POLR2A	chr1:113240720-113241982	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr1:113240783-113246836	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr1:113240809-113241812	HepG2	liver:	n/a	n/a
33	POLR2A	chr1:113240910-113241829	GM12892	blood:	n/a	n/a
34	POLR2A	chr1:113240988-113241763	U87	brain:	n/a	n/a
35	POLR2A	chr1:113240610-113244540	HepG2	liver:	n/a	n/a
36	POLR2A	chr1:113240176-113246017	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr1:113240249-113248607	HepG2	liver:	n/a	n/a
38	POLR2A	chr1:113240688-113241670	IMR90	lung:	n/a	n/a
39	POLR2A	chr1:113241052-113245981	K562	blood:	n/a	n/a
40	POLR2A	chr1:113240102-113248913	U87	brain:	n/a	n/a
41	NFIC	chr1:113240966-113241854	HepG2	liver:	n/a	n/a
42	POLR2A	chr1:113240904-113241810	GM12892	blood:	n/a	n/a
43	POLR2A	chr1:113240145-113241880	MCF10A-Er-Src	breast:	n/a	n/a
44	EGR1	chr1:113240859-113241273	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113159779..113171222-chr1:113238237..113251191,41	K562	blood:
2	chr1:113214866..113222565-chr1:113237012..113253952,54	K562	blood:
3	chr1:113160176..113163931-chr1:113238020..113242018,6	K562	blood:
4	chr1:113239573..113244483-chr1:113252369..113259292,10	K562	blood:
5	chr1:112937855..112940278-chr1:113239914..113242532,2	MCF-7	breast:
6	chr1:113240296..113243095-chr1:113496225..113498995,2	K562	blood:
7	chr1:113215224..113219998-chr1:113238829..113244717,20	MCF-7	breast:
8	chr1:113214002..113222947-chr1:113236890..113251579,47	MCF-7	breast:
9	chr1:113156746..113166477-chr1:113240630..113253423,46	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000225075	TF binding region
MOV10	TF binding region
ENSG00000007341	Chromatin interaction
ENSG00000155367	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000271810	Chromatin interaction
ENSG00000155380	Chromatin interaction
ENSG00000235299	Chromatin interaction
ENSG00000261595	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000143079	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1106287	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1110042	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102513	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11102514	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11102520	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12030612	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12030641	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12040988	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12049572	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12120956	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12122980	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12126684	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12126971	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12130243	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12133583	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137269	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs12406282	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728311	0.84[EUR][1000 genomes]
rs12756815	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17030613	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17030651	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2009056	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2273368	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs2279499	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2306937	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2887882	0.87[EUR][1000 genomes]
rs34848593	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737136	0.94[CEU][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs3748656	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795819	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61818802	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61818805	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6679	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs883593	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308256	0.80[AMR][1000 genomes];0.87[EUR][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	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
8	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
9	esv997362	chr1:113234820-113243297	Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2306940	ST7L	cis	lymphoblastoid	seeQTL
rs2306940	SLC16A4	cis	cerebellum	SCAN
rs2306940	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs2306940	CAPZA1	cis	cerebellum	SCAN
rs2306940	AMPD1	cis	cerebellum	SCAN
rs2306940	WNT2B	cis	parietal	SCAN
rs2306940	SYT6	cis	parietal	SCAN
rs2306940	GSTM2	cis	parietal	SCAN
rs2306940	ST7L	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113219000-113242200	Weak transcription	NHDF-Ad	bronchial
2	chr1:113219000-113243800	Weak transcription	Fetal Brain Male	brain
3	chr1:113222000-113243000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:113228600-113242800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:113228600-113242800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr1:113229000-113242200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:113229200-113248000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:113229600-113243200	Strong transcription	Dnd41	blood
9	chr1:113230200-113241200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:113230200-113242600	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:113230200-113243000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:113230200-113243200	Strong transcription	Primary T cells from cord blood	blood
13	chr1:113230400-113241200	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:113230600-113241400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:113230600-113242000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:113230600-113242000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:113230600-113242200	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:113230600-113242600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr1:113230800-113241400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:113231200-113241400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:113231400-113241800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:113231600-113241200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:113231600-113243000	Weak transcription	Psoas Muscle	Psoas
24	chr1:113231600-113243200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:113231800-113242400	Strong transcription	Osteobl	bone
26	chr1:113231800-113242600	Strong transcription	Fetal Lung	lung
27	chr1:113232000-113241400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:113232000-113242400	Strong transcription	Fetal Stomach	stomach
29	chr1:113232000-113242600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:113232200-113241400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:113232200-113241800	Strong transcription	Colon Smooth Muscle	Colon
32	chr1:113232200-113241800	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:113232400-113242000	Strong transcription	Brain Hippocampus Middle	brain
34	chr1:113232400-113242600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:113232600-113241200	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:113233000-113242200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr1:113234000-113241200	Strong transcription	Brain Cingulate Gyrus	brain
38	chr1:113234000-113241600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:113234000-113242800	Strong transcription	Brain Anterior Caudate	brain
40	chr1:113234000-113244400	Strong transcription	Thymus	Thymus
41	chr1:113234200-113241200	Strong transcription	Rectal Smooth Muscle	rectum
42	chr1:113234200-113241600	Strong transcription	Aorta	Aorta
43	chr1:113234200-113242200	Strong transcription	Esophagus	oesophagus
44	chr1:113234200-113242400	Strong transcription	NHLF	lung
45	chr1:113234200-113242600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:113234200-113242800	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr1:113234400-113241800	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr1:113234400-113242800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:113235600-113242200	Weak transcription	Fetal Brain Female	brain
50	chr1:113235800-113241200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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