Variant report

Variant	rs9630962
Chromosome Location	chr2:234293499-234293500
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	FOXA1	chr2:234293377-234293820	HepG2	liver:	n/a	n/a
2	MYC	chr2:234293366-234293731	MCF10A-Er-Src	breast:	n/a	chr2:234293701-234293710
3	POLR2A	chr2:234293034-234295804	GM18505	blood:	n/a	n/a
4	POLR2A	chr2:234293276-234294756	GM15510	blood:	n/a	n/a
5	FOXA1	chr2:234293476-234293836	HepG2	liver:	n/a	n/a
6	FOXA1	chr2:234293321-234293845	HepG2	liver:	n/a	n/a
7	ELF1	chr2:234293417-234294382	GM12878	blood:	n/a	n/a
8	FOS	chr2:234293454-234293552	MCF10A-Er-Src	breast:	n/a	n/a
9	MYC	chr2:234293431-234293825	MCF10A-Er-Src	breast:	n/a	chr2:234293701-234293710
10	POLR2A	chr2:234293493-234294860	GM12892	blood:	n/a	n/a
11	FOXA2	chr2:234293415-234293722	HepG2	liver:	n/a	n/a
12	STAT3	chr2:234293446-234293642	MCF10A-Er-Src	breast:	n/a	n/a
13	FOXA1	chr2:234293384-234293785	HepG2	liver:	n/a	n/a
14	MAX	chr2:234293480-234294021	HepG2	liver:	n/a	chr2:234293879-234293888 chr2:234293880-234293887 chr2:234293701-234293710
15	POLR2A	chr2:234293409-234294421	GM12892	blood:	n/a	n/a
16	FOXA2	chr2:234293493-234293888	A549	lung:	n/a	n/a
17	MTA3	chr2:234293391-234295254	GM12878	blood:	n/a	n/a
18	CTCF	chr2:234293460-234293610	HRE	kidney:	n/a	n/a
19	MAX	chr2:234293362-234294525	A549	lung:	n/a	chr2:234294330-234294337 chr2:234293879-234293888 chr2:234293880-234293887 chr2:234293701-234293710 chr2:234294329-234294338
20	POLR2A	chr2:234293343-234297175	GM12891	blood:	n/a	n/a
21	POLR2A	chr2:234293457-234293756	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234259434..234265610-chr2:234290886..234296562,9	MCF-7	breast:
2	chr2:234292070..234294223-chr2:234599510..234601905,2	MCF-7	breast:
3	chr2:234289741..234291350-chr2:234292115..234294515,2	K562	blood:

Variant related genes	Relation type
DGKD	TF binding region
ENSG00000201013	TF binding region
ENSG00000259793	Chromatin interaction
ENSG00000077044	Chromatin interaction
ENSG00000243637	Chromatin interaction
ENSG00000167165	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10184680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10190563	1.00[AMR][1000 genomes]
rs12328351	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12329282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13391971	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13396948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13400041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13403632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13410746	0.83[AMR][1000 genomes]
rs13415216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13415911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13415978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13416999	1.00[AMR][1000 genomes]
rs13419047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13427191	1.00[AMR][1000 genomes]
rs58351001	0.83[AMR][1000 genomes]
rs59075316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59292380	0.83[AMR][1000 genomes]
rs59357220	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60341933	0.83[AMR][1000 genomes]
rs61006258	0.83[AMR][1000 genomes]
rs73106640	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73106643	0.83[AMR][1000 genomes]
rs73106659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73106660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73106663	0.83[AMR][1000 genomes]
rs73115369	0.83[AMR][1000 genomes]
rs73115377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73115389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234264600-234307600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:234265000-234295000	Weak transcription	Osteobl	bone
3	chr2:234265200-234295000	Weak transcription	NH-A	brain
4	chr2:234266400-234294000	Weak transcription	Fetal Brain Male	brain
5	chr2:234270000-234322400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:234272800-234313200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:234274000-234295200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:234277600-234322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:234278600-234293600	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:234278600-234293800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:234278600-234294000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:234278600-234294000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:234279200-234293600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:234279200-234294400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:234280400-234294800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:234281800-234296600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:234282200-234293600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:234282400-234294400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:234282400-234298000	Weak transcription	Dnd41	blood
20	chr2:234284000-234293800	Weak transcription	Colonic Mucosa	Colon
21	chr2:234284800-234295400	Weak transcription	Fetal Intestine Large	intestine
22	chr2:234285000-234295400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr2:234287400-234294800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr2:234289000-234307600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:234289600-234294600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr2:234290000-234293600	Weak transcription	Spleen	Spleen
27	chr2:234290200-234294800	Weak transcription	Small Intestine	intestine
28	chr2:234290600-234297000	Enhancers	Primary T cells fromperipheralblood	blood
29	chr2:234290800-234294000	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr2:234290800-234296800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr2:234291000-234297000	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr2:234291200-234295800	Enhancers	Thymus	Thymus
33	chr2:234291600-234293600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:234291800-234293600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:234292000-234297200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:234292200-234294000	Enhancers	Primary T cells from cord blood	blood
37	chr2:234292200-234294400	Genic enhancers	Primary monocytes fromperipheralblood	blood
38	chr2:234292200-234294400	Enhancers	Ovary	ovary
39	chr2:234292200-234296400	Enhancers	Primary hematopoietic stem cells	blood
40	chr2:234292200-234296600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr2:234292200-234297200	Enhancers	Fetal Heart	heart
42	chr2:234292200-234297200	Enhancers	Left Ventricle	heart
43	chr2:234292400-234293800	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr2:234292400-234294600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:234292400-234294800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:234292400-234295800	Enhancers	K562	blood
47	chr2:234292400-234296000	Enhancers	Fetal Lung	lung
48	chr2:234292400-234296200	Enhancers	HepG2	liver
49	chr2:234292400-234296800	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr2:234292400-234297200	Enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links