Variant report

Variant	rs12078414
Chromosome Location	chr1:9885290-9885291
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr1:9882936-9885905	K562	blood:	n/a	chr1:9884875-9884885 chr1:9883243-9883253
2	TFAP2C	chr1:9884475-9886102	Hela-S3	cervix:	n/a	chr1:9885741-9885756
3	NFIC	chr1:9884933-9885976	ECC-1	luminal epithelium:	n/a	n/a
4	TCF7L2	chr1:9885107-9885978	Hela-S3	cervix:	n/a	n/a
5	FOXA2	chr1:9885144-9885905	A549	lung:	n/a	n/a
6	HDAC2	chr1:9885246-9886021	MCF-7	breast:	n/a	n/a
7	RCOR1	chr1:9883718-9885814	K562	blood:	n/a	n/a
8	POLR2A	chr1:9885214-9886045	Hela-S3	cervix:	n/a	n/a
9	EP300	chr1:9884949-9886117	ECC-1	luminal epithelium:	n/a	chr1:9885810-9885819
10	MAX	chr1:9885072-9886004	Hela-S3	cervix:	n/a	n/a
11	MXI1	chr1:9885056-9885949	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:9885245-9886110	Hela-S3	cervix:	n/a	n/a
13	YY1	chr1:9885223-9885754	HCT-116	colon:	n/a	n/a
14	NFIC	chr1:9884878-9885923	ECC-1	luminal epithelium:	n/a	n/a
15	KAP1	chr1:9884841-9886021	HEK293	kidney:	n/a	chr1:9885607-9885616
16	SP1	chr1:9885132-9885881	H1-hESC	embryonic stem cell:	n/a	chr1:9885811-9885825 chr1:9885491-9885502 chr1:9885575-9885585 chr1:9885493-9885502 chr1:9885726-9885740 chr1:9885575-9885585
17	TFAP2A	chr1:9885174-9886067	Hela-S3	cervix:	n/a	chr1:9885743-9885758
18	POLR2A	chr1:9885208-9886220	Hela-S3	cervix:	n/a	n/a
19	ZBTB7A	chr1:9884232-9885903	ECC-1	luminal epithelium:	n/a	n/a
20	JUND	chr1:9885054-9885906	Hela-S3	cervix:	n/a	chr1:9885607-9885614 chr1:9885606-9885614 chr1:9885335-9885349
21	BRCA1	chr1:9885056-9885968	Hela-S3	cervix:	n/a	n/a
22	SMC3	chr1:9885114-9886000	Hela-S3	cervix:	n/a	chr1:9885179-9885189 chr1:9885650-9885660
23	RFX5	chr1:9885038-9886177	Hela-S3	cervix:	n/a	chr1:9885633-9885650
24	GATA3	chr1:9885247-9886086	A549	lung:	n/a	n/a
25	CHD2	chr1:9885052-9886152	Hela-S3	cervix:	n/a	n/a
26	TCF12	chr1:9884608-9886108	A549	lung:	n/a	chr1:9884869-9884879 chr1:9885486-9885496
27	RCOR1	chr1:9884826-9885514	HepG2	liver:	n/a	n/a
28	MAZ	chr1:9884892-9886063	Hela-S3	cervix:	n/a	n/a
29	FOSL2	chr1:9885136-9886159	A549	lung:	n/a	chr1:9885607-9885614 chr1:9885606-9885614 chr1:9885335-9885349
30	RCOR1	chr1:9884838-9886091	Hela-S3	cervix:	n/a	n/a
31	ELF1	chr1:9885074-9885951	GM12878	blood:	n/a	chr1:9885810-9885821
32	SP1	chr1:9884921-9886064	A549	lung:	n/a	chr1:9885811-9885825 chr1:9885491-9885502 chr1:9885575-9885585 chr1:9885493-9885502 chr1:9885726-9885740 chr1:9885575-9885585
33	STAT3	chr1:9884978-9885918	Hela-S3	cervix:	n/a	chr1:9885610-9885622 chr1:9885874-9885881 chr1:9885475-9885487
34	USF2	chr1:9885226-9885893	Hela-S3	cervix:	n/a	n/a
35	MAX	chr1:9885118-9886032	Hela-S3	cervix:	n/a	n/a
36	RAD21	chr1:9885189-9886053	Hela-S3	cervix:	n/a	chr1:9885616-9885626 chr1:9885456-9885465
37	TCF12	chr1:9885262-9886053	ECC-1	luminal epithelium:	n/a	chr1:9885486-9885496
38	SP1	chr1:9884965-9886075	A549	lung:	n/a	chr1:9885811-9885825 chr1:9885491-9885502 chr1:9885575-9885585 chr1:9885493-9885502 chr1:9885726-9885740 chr1:9885575-9885585
39	POLR2A	chr1:9885202-9886081	Hela-S3	cervix:	n/a	n/a
40	KAP1	chr1:9885060-9886017	U2OS	brain:	n/a	chr1:9885607-9885616
41	SP1	chr1:9884882-9886285	HCT-116	colon:	n/a	chr1:9885811-9885825 chr1:9885491-9885502 chr1:9885575-9885585 chr1:9885493-9885502 chr1:9885726-9885740 chr1:9885575-9885585
42	TBP	chr1:9885210-9886171	Hela-S3	cervix:	n/a	n/a
43	ELK1	chr1:9885157-9886020	Hela-S3	cervix:	n/a	n/a
44	ELF1	chr1:9885199-9886172	MCF-7	breast:	n/a	chr1:9885810-9885821
45	ZNF263	chr1:9884880-9886108	HEK293-T-REx	kidney:	n/a	chr1:9885987-9885996 chr1:9885770-9885791
46	HA-E2F1	chr1:9884204-9885860	MCF-7	breast:	n/a	chr1:9884435-9884444
47	CEBPB	chr1:9885175-9885856	Hela-S3	cervix:	n/a	n/a
48	GTF2F1	chr1:9885055-9885960	Hela-S3	cervix:	n/a	n/a
49	JUND	chr1:9885129-9885826	A549	lung:	n/a	chr1:9885607-9885614 chr1:9885606-9885614 chr1:9885335-9885349
50	EP300	chr1:9884976-9885883	Hela-S3	cervix:	n/a	chr1:9885810-9885819

No.	Distal block	Cell Line	Cell type
1	chr1:9884569..9887155-chr1:10002902..10004455,2	K562	blood:
2	chr1:9852615..9854985-chr1:9884936..9886688,2	MCF-7	breast:
3	chr1:9882501..9887964-chr1:9906388..9911794,10	MCF-7	breast:
4	chr1:9884699..9887504-chr1:9972988..9975946,2	K562	blood:

Variant related genes	Relation type
CLSTN1	TF binding region
ENSG00000162441	Chromatin interaction
ENSG00000223989	Chromatin interaction
ENSG00000173614	Chromatin interaction
ENSG00000228150	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10779731	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs10864436	1.00[CEU][hapmap]
rs10864437	0.88[EUR][1000 genomes]
rs10864438	0.93[EUR][1000 genomes]
rs11121486	0.85[CEU][hapmap]
rs11121490	0.86[EUR][1000 genomes]
rs11121492	1.00[CEU][hapmap]
rs11121493	1.00[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs11674	0.86[EUR][1000 genomes]
rs11806520	0.89[EUR][1000 genomes]
rs12037599	0.85[CEU][hapmap]
rs12042293	0.85[CEU][hapmap]
rs12047054	1.00[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs12068489	0.91[ASN][1000 genomes]
rs12087051	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12088273	0.88[EUR][1000 genomes]
rs1220386	0.82[ASN][1000 genomes]
rs1228434	0.82[EUR][1000 genomes]
rs12568720	0.94[ASW][hapmap];0.85[CEU][hapmap]
rs12569008	0.88[ASW][hapmap];0.85[CEU][hapmap]
rs1615629	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs1631962	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1660738	0.93[ASN][1000 genomes]
rs1660741	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1660742	1.00[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs17034335	1.00[CEU][hapmap]
rs1767277	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2582979	0.93[ASN][1000 genomes]
rs2788605	0.87[EUR][1000 genomes]
rs4585981	0.87[EUR][1000 genomes]
rs56109009	0.86[EUR][1000 genomes]
rs57480158	0.80[EUR][1000 genomes]
rs57560942	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59729812	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6699320	1.00[CEU][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs72855716	0.93[EUR][1000 genomes]
rs72855733	0.85[EUR][1000 genomes]
rs72855735	0.87[EUR][1000 genomes]
rs72855745	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72855747	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526958	0.88[ASW][hapmap];0.85[CEU][hapmap]
rs7550246	0.86[EUR][1000 genomes]
rs7550295	0.85[CEU][hapmap]
rs767762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs935071	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs946277	0.80[EUR][1000 genomes]
rs946278	0.80[EUR][1000 genomes]
rs946279	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv3330047	chr1:9882590-9885538	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	esv3431219	chr1:9882990-9885488	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9882400-9885600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr1:9882600-9885400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:9884200-9886200	Flanking Active TSS	Hela-S3	cervix
4	chr1:9884400-9885400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:9884400-9885400	Enhancers	Fetal Lung	lung
6	chr1:9884400-9885600	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr1:9884400-9885600	Flanking Active TSS	Colonic Mucosa	Colon
8	chr1:9884400-9885600	Enhancers	Fetal Heart	heart
9	chr1:9884400-9885600	Flanking Active TSS	HMEC	breast
10	chr1:9884400-9885600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr1:9884400-9885800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:9884400-9885800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:9884400-9885800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr1:9884400-9886000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr1:9884400-9886000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:9884400-9886000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:9884400-9886200	Flanking Active TSS	NHEK	skin
18	chr1:9884600-9885400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr1:9884600-9885400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr1:9884600-9885400	Flanking Bivalent TSS/Enh	HepG2	liver
21	chr1:9884600-9885600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:9884600-9885600	Enhancers	Liver	Liver
23	chr1:9884600-9885600	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr1:9884600-9885800	Enhancers	Lung	lung
25	chr1:9884600-9885800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr1:9884600-9885800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr1:9884600-9885800	Enhancers	Spleen	Spleen
28	chr1:9884600-9886000	Enhancers	Primary T cells from cord blood	blood
29	chr1:9884600-9886200	Flanking Active TSS	A549	lung
30	chr1:9884800-9885400	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
31	chr1:9884800-9885400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:9884800-9885400	Enhancers	Aorta	Aorta
33	chr1:9884800-9885400	Flanking Active TSS	Brain Angular Gyrus	brain
34	chr1:9884800-9885400	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr1:9884800-9885400	Weak transcription	Fetal Kidney	kidney
36	chr1:9884800-9885400	Bivalent Enhancer	Thymus	Thymus
37	chr1:9884800-9885600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
38	chr1:9884800-9885600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr1:9884800-9885600	Bivalent Enhancer	Fetal Thymus	thymus
40	chr1:9884800-9885600	Flanking Active TSS	Right Ventricle	heart
41	chr1:9884800-9885800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:9884800-9885800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:9884800-9885800	Enhancers	Fetal Stomach	stomach
44	chr1:9884800-9885800	Enhancers	Psoas Muscle	Psoas
45	chr1:9884800-9885800	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr1:9884800-9885800	Weak transcription	HSMMtube	muscle
47	chr1:9884800-9885800	Bivalent Enhancer	K562	blood
48	chr1:9884800-9886000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:9884800-9886000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
50	chr1:9884800-9886000	Enhancers	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links