Variant report

Variant	rs17035912
Chromosome Location	chr2:47171322-47171323
allele	A/G
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	BCL11A	chr2:47170996-47171553	GM12878	blood:	n/a	chr2:47171253-47171262
2	MXI1	chr2:47170417-47171396	GM12878	blood:	n/a	chr2:47170887-47170896
3	PML	chr2:47170238-47171843	GM12878	blood:	n/a	n/a
4	BCLAF1	chr2:47170815-47171789	GM12878	blood:	n/a	chr2:47171253-47171262
5	ATF2	chr2:47171000-47171729	GM12878	blood:	n/a	n/a
6	FOXM1	chr2:47170404-47171603	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:47170932-47171329	GM12891	blood:	n/a	n/a
8	TAF1	chr2:47170959-47171372	GM12878	blood:	n/a	n/a
9	RELA	chr2:47170344-47171702	GM19099	blood:	n/a	n/a
10	POLR2A	chr2:47170331-47171329	GM12891	blood:	n/a	n/a
11	EBF1	chr2:47171039-47171438	GM12878	blood:	n/a	n/a
12	TBL1XR1	chr2:47171113-47171494	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:47169934-47171448	GM12892	blood:	n/a	n/a
14	POLR2A	chr2:47170434-47171393	GM12892	blood:	n/a	n/a
15	STAT5A	chr2:47170996-47171806	GM12878	blood:	n/a	n/a
16	NFATC1	chr2:47170896-47171620	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:47170199-47171419	GM12892	blood:	n/a	n/a
18	EP300	chr2:47170737-47171427	GM12878	blood:	n/a	n/a
19	ELK1	chr2:47170829-47171374	GM12878	blood:	n/a	n/a
20	STAT5A	chr2:47171083-47171773	GM12878	blood:	n/a	n/a
21	POLR2A	chr2:47170194-47171484	GM12892	blood:	n/a	n/a
22	POLR2A	chr2:47168094-47171520	GM12878	blood:	n/a	n/a
23	NFIC	chr2:47170791-47171793	GM12878	blood:	n/a	n/a
24	EP300	chr2:47170918-47171487	GM12878	blood:	n/a	n/a
25	SP1	chr2:47171114-47171559	GM12878	blood:	n/a	n/a
26	SP1	chr2:47170989-47171498	GM12878	blood:	n/a	n/a
27	WRNIP1	chr2:47170350-47171496	GM12878	blood:	n/a	n/a
28	RUNX3	chr2:47170251-47171811	GM12878	blood:	n/a	n/a
29	RELA	chr2:47170635-47171543	GM18951	blood:	n/a	n/a
30	CHD2	chr2:47170755-47171371	GM12878	blood:	n/a	n/a
31	BCLAF1	chr2:47170998-47171824	GM12878	blood:	n/a	chr2:47171253-47171262
32	RELA	chr2:47170644-47171592	GM12878	blood:	n/a	n/a
33	EBF1	chr2:47170932-47171357	GM12878	blood:	n/a	n/a
34	RELA	chr2:47170558-47171714	GM18505	blood:	n/a	n/a
35	STAT3	chr2:47171027-47171465	GM12878	blood:	n/a	n/a
36	CEBPB	chr2:47170856-47171690	GM12878	blood:	n/a	n/a
37	ATF2	chr2:47170833-47171685	GM12878	blood:	n/a	n/a
38	TBP	chr2:47170793-47171547	GM12878	blood:	n/a	n/a
39	MAZ	chr2:47170990-47171497	GM12878	blood:	n/a	n/a
40	POLR2A	chr2:47170307-47171409	GM12878	blood:	n/a	n/a
41	RELA	chr2:47170580-47171561	GM12892	blood:	n/a	n/a
42	ZEB1	chr2:47171047-47171337	GM12878	blood:	n/a	n/a
43	ETS1	chr2:47170951-47171325	GM12878	blood:	n/a	chr2:47171217-47171232 chr2:47171220-47171229 chr2:47171220-47171229 chr2:47171220-47171229 chr2:47171217-47171233 chr2:47171220-47171229
44	ZNF384	chr2:47170996-47171765	GM12878	blood:	n/a	n/a
45	POLR2A	chr2:47168084-47171676	GM12878	blood:	n/a	n/a
46	BATF	chr2:47171013-47171486	GM12878	blood:	n/a	n/a
47	POLR2A	chr2:47168238-47171702	GM12891	blood:	n/a	n/a
48	RCOR1	chr2:47171006-47171732	GM12878	blood:	n/a	n/a
49	MTA3	chr2:47170073-47172114	GM12878	blood:	n/a	n/a
50	RELA	chr2:47170898-47171450	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:47170300..47176373-chr2:47180929..47185322,6	MCF-7	breast:
2	chr2:47169747..47171383-chr2:47233270..47235359,2	MCF-7	breast:
3	chr2:47168340..47172583-chr2:47183123..47189203,6	MCF-7	breast:

Variant related genes	Relation type
MCFD2	TF binding region
ENSG00000272814	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10084332	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1010724	0.89[YRI][hapmap]
rs10164756	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10165085	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10181411	0.92[AMR][1000 genomes]
rs10186980	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10199965	0.87[CEU][hapmap]
rs11894319	0.87[CEU][hapmap]
rs11897050	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs13388612	0.87[CEU][hapmap]
rs13391660	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13398748	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13406024	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13407588	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13409489	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13417753	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs13423962	0.87[CEU][hapmap]
rs13424086	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13430346	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13430703	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17035878	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17035887	0.87[CEU][hapmap]
rs28405928	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28465613	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28529158	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28612371	0.95[EUR][1000 genomes]
rs28770495	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4300885	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4314044	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4583513	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6729569	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6743966	0.87[CEU][hapmap]
rs6755386	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6758093	0.86[CEU][hapmap]
rs73926967	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73926970	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73926978	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73926980	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73926983	1.00[EUR][1000 genomes]
rs73926986	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73926988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7577816	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7586004	0.87[CEU][hapmap]
rs7603884	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9973769	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS 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	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47168600-47171400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:47169000-47171400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
3	chr2:47169000-47171400	Flanking Active TSS	Brain Hippocampus Middle	brain
4	chr2:47169000-47171600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr2:47169400-47171800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr2:47169400-47178800	Weak transcription	Ovary	ovary
7	chr2:47169400-47179000	Weak transcription	Gastric	stomach
8	chr2:47169600-47171600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:47169600-47172000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:47169600-47172800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr2:47169600-47175000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:47169600-47177600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:47169600-47177600	Weak transcription	Left Ventricle	heart
14	chr2:47169600-47178800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:47169600-47183600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:47169800-47171400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr2:47169800-47171400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:47169800-47171600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:47169800-47171600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:47169800-47171600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr2:47169800-47171800	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
22	chr2:47169800-47172800	Weak transcription	Fetal Heart	heart
23	chr2:47169800-47177600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr2:47169800-47177600	Weak transcription	Fetal Lung	lung
25	chr2:47169800-47178200	Weak transcription	Fetal Brain Female	brain
26	chr2:47169800-47182000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:47169800-47182200	Weak transcription	Right Ventricle	heart
28	chr2:47169800-47214600	Weak transcription	Fetal Kidney	kidney
29	chr2:47170000-47171400	Enhancers	Brain Cingulate Gyrus	brain
30	chr2:47170000-47171400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:47170000-47171600	Enhancers	Placenta	Placenta
32	chr2:47170000-47171800	Enhancers	Pancreas	Pancrea
33	chr2:47170000-47171800	Enhancers	Spleen	Spleen
34	chr2:47170000-47177000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr2:47170000-47177400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:47170000-47177600	Weak transcription	Esophagus	oesophagus
37	chr2:47170000-47177800	Weak transcription	Liver	Liver
38	chr2:47170000-47177800	Weak transcription	NH-A	brain
39	chr2:47170000-47178800	Weak transcription	HSMMtube	muscle
40	chr2:47170000-47181600	Weak transcription	HUVEC	blood vessel
41	chr2:47170000-47182200	Weak transcription	Psoas Muscle	Psoas
42	chr2:47170200-47171400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:47170200-47171400	Enhancers	Colon Smooth Muscle	Colon
44	chr2:47170200-47172200	Weak transcription	Fetal Intestine Small	intestine
45	chr2:47170200-47177600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:47170200-47181400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:47170400-47171400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:47170400-47171400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:47170400-47177400	Weak transcription	Fetal Intestine Large	intestine
50	chr2:47170600-47171400	Enhancers	HepG2	liver

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