Variant report

Variant	rs7609233
Chromosome Location	chr2:39664825-39664826
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	RCOR1	chr2:39662966-39665554	K562	blood:	n/a	n/a
2	MAX	chr2:39663407-39665631	HCT-116	colon:	n/a	chr2:39665266-39665277 chr2:39665266-39665275 chr2:39665267-39665276 chr2:39665267-39665274
3	SIN3A	chr2:39663124-39665275	H1-hESC	embryonic stem cell:	n/a	chr2:39664207-39664220
4	REST	chr2:39663223-39665181	H1-neurons	neurons:	n/a	chr2:39664865-39664878 chr2:39664436-39664449
5	POLR2A	chr2:39663973-39665248	GM19099	blood:	n/a	n/a
6	TAF1	chr2:39663509-39664850	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr2:39663493-39664898	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr2:39663743-39665341	GM12892	blood:	n/a	n/a
9	POLR2A	chr2:39663908-39665084	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr2:39663605-39665389	Raji	blood:	n/a	n/a
11	BHLHE40	chr2:39664323-39665452	GM12878	blood:	n/a	n/a
12	HA-E2F1	chr2:39663563-39665415	MCF-7	breast:	n/a	chr2:39664008-39664017 chr2:39664312-39664321
13	POLR2A	chr2:39663887-39664895	GM12892	blood:	n/a	n/a
14	BRCA1	chr2:39664308-39665474	Hela-S3	cervix:	n/a	n/a
15	HNF4A	chr2:39664184-39664897	HepG2	liver:	n/a	chr2:39664756-39664768 chr2:39664755-39664768 chr2:39664755-39664763
16	POLR2A	chr2:39663994-39664877	SK-N-SH	brain:	n/a	n/a
17	HEY1	chr2:39663513-39665303	HepG2	liver:	n/a	chr2:39664493-39664508
18	UBTF	chr2:39662309-39665492	K562	blood:	n/a	n/a
19	HDAC2	chr2:39663819-39665385	HepG2	liver:	n/a	n/a
20	MTA3	chr2:39664502-39665520	GM12878	blood:	n/a	n/a
21	MAX	chr2:39663944-39664893	HepG2	liver:	n/a	n/a
22	POLR2A	chr2:39663492-39665476	HepG2	liver:	n/a	n/a
23	HMGN3	chr2:39663658-39665164	K562	blood:	n/a	n/a
24	CREB1	chr2:39663513-39665577	HepG2	liver:	n/a	n/a
25	POLR2A	chr2:39663591-39665410	GM19193	blood:	n/a	n/a
26	EP300	chr2:39663635-39665271	SK-N-SH	brain:	n/a	chr2:39664010-39664026
27	YY1	chr2:39663508-39664918	SK-N-SH_RA	brain:	n/a	chr2:39664495-39664509 chr2:39664414-39664422
28	POLR2A	chr2:39664214-39664859	SK-N-MC	brain:	n/a	n/a
29	TBP	chr2:39663692-39664863	HepG2	liver:	n/a	n/a
30	CEBPD	chr2:39663958-39664867	HepG2	liver:	n/a	n/a
31	POLR2A	chr2:39663595-39665532	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr2:39663840-39665394	GM15510	blood:	n/a	n/a
33	POLR2A	chr2:39663449-39665118	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr2:39663532-39665508	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr2:39663898-39665337	K562	blood:	n/a	n/a
36	SMC3	chr2:39664733-39664931	HepG2	liver:	n/a	n/a
37	TEAD4	chr2:39663780-39664894	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr2:39663956-39664949	HUVEC	blood vessel:	n/a	n/a
39	EP300	chr2:39663559-39664835	HepG2	liver:	n/a	chr2:39664010-39664026
40	CBX3	chr2:39664210-39664877	K562	blood:	n/a	n/a
41	POLR2A	chr2:39663734-39666027	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr2:39663883-39665533	Hela-S3	cervix:	n/a	n/a
43	ARID3A	chr2:39663932-39665347	HepG2	liver:	n/a	n/a
44	SIN3AK20	chr2:39663832-39665249	PANC-1	pancreas:	n/a	n/a
45	REST	chr2:39664315-39664886	A549	lung:	n/a	chr2:39664865-39664878 chr2:39664436-39664449
46	POLR2A	chr2:39664045-39664829	PANC-1	pancreas:	n/a	n/a
47	MXI1	chr2:39662210-39666175	SK-N-SH	brain:	n/a	n/a
48	GATA3	chr2:39664005-39665375	A549	lung:	n/a	n/a
49	YY1	chr2:39663471-39665286	HepG2	liver:	n/a	chr2:39664495-39664509 chr2:39664414-39664422
50	POLR2A	chr2:39663801-39665367	GM18526	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:149858090..149858876-chr2:39664075..39665067,2	Hela-S3	cervix:
2	chr2:39603738..39609073-chr2:39660426..39665645,8	MCF-7	breast:
3	chr17:43236605..43238756-chr2:39663829..39665960,2	MCF-7	breast:
4	chr2:39601552..39609752-chr2:39662569..39667062,10	MCF-7	breast:
5	chr2:39664730..39667183-chr2:39678037..39681016,2	MCF-7	breast:
6	chr2:39619324..39621910-chr2:39662875..39665257,2	K562	blood:

Variant related genes	Relation type
MAP4K3	TF binding region
ENSG00000224505	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000252239	Chromatin interaction
ENSG00000231312	Chromatin interaction
ENSG00000168517	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000011566	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12105018	1.00[AMR][1000 genomes]
rs57107827	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs57164521	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs58019817	0.91[AMR][1000 genomes]
rs61344670	0.82[AMR][1000 genomes]
rs6706951	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6722096	0.91[AMR][1000 genomes]
rs6725496	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6725704	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6732290	0.88[YRI][hapmap]
rs6759388	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72914206	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs72925278	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72925283	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72925290	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72927103	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72927107	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72927108	0.91[AMR][1000 genomes]
rs72927110	0.91[AMR][1000 genomes]
rs72927119	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72927143	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72929164	1.00[AMR][1000 genomes]
rs72929184	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72931129	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72931131	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72931135	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72931145	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72931150	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72931159	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72931161	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs72931172	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7566368	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7581123	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7592925	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv2695	chr2:39643221-39688015	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39661000-39666000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:39661200-39665000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:39661400-39665000	Active TSS	Right Atrium	heart
4	chr2:39661800-39665200	Active TSS	HSMMtube	muscle
5	chr2:39661800-39667000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:39661800-39667000	Active TSS	Aorta	Aorta
7	chr2:39662000-39665000	Active TSS	Stomach Smooth Muscle	stomach
8	chr2:39662000-39665200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:39662000-39665200	Active TSS	NHLF	lung
10	chr2:39662000-39665400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:39662000-39665400	Active TSS	HSMM	muscle
12	chr2:39662000-39665600	Active TSS	Right Ventricle	heart
13	chr2:39662000-39665800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr2:39662000-39666000	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr2:39662000-39666200	Active TSS	Ovary	ovary
16	chr2:39662200-39665600	Active TSS	Fetal Muscle Trunk	muscle
17	chr2:39662400-39665200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:39662400-39665200	Active TSS	H9 Cell Line	embryonic stem cell
19	chr2:39662400-39665200	Active TSS	Brain Hippocampus Middle	brain
20	chr2:39662400-39665200	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr2:39662400-39665200	Bivalent/Poised TSS	HepG2	liver
22	chr2:39662400-39665400	Active TSS	Colonic Mucosa	Colon
23	chr2:39662400-39665600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr2:39662400-39665600	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr2:39662400-39665600	Active TSS	Lung	lung
26	chr2:39662400-39665600	Active TSS	NHDF-Ad	bronchial
27	chr2:39662400-39666000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:39662600-39665000	Active TSS	H1 Cell Line	embryonic stem cell
29	chr2:39662600-39665000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:39662600-39665200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:39662600-39665200	Active TSS	Fetal Kidney	kidney
32	chr2:39662600-39665200	Active TSS	Fetal Stomach	stomach
33	chr2:39662600-39665400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:39662600-39665400	Active TSS	Brain Cingulate Gyrus	brain
35	chr2:39662600-39665400	Active TSS	Gastric	stomach
36	chr2:39662600-39665400	Active TSS	Rectal Smooth Muscle	rectum
37	chr2:39662600-39665600	Active TSS	Brain Substantia Nigra	brain
38	chr2:39662600-39665600	Active TSS	Psoas Muscle	Psoas
39	chr2:39662600-39665600	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr2:39662600-39666000	Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr2:39662600-39666000	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr2:39662800-39665000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:39662800-39665000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:39662800-39665000	Active TSS	Muscle Satellite Cultured Cells	--
45	chr2:39662800-39665000	Active TSS	Fetal Muscle Leg	muscle
46	chr2:39662800-39665000	Active TSS	Placenta	Placenta
47	chr2:39662800-39665000	Active TSS	Osteobl	bone
48	chr2:39662800-39665200	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr2:39662800-39665200	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr2:39662800-39665200	Active TSS	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links