Variant report

Variant	rs7978723
Chromosome Location	chr12:51448918-51448919
allele	A/C
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	POLR2A	chr12:51448563-51449185	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:51448825-51449198	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr12:51448889-51449191	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:51446371..51449109-chr12:51475954..51477544,3	K562	blood:
2	chr12:51446671..51449109-chr12:51475852..51477454,2	K562	blood:
3	chr12:51440743..51444863-chr12:51448295..51453075,7	MCF-7	breast:
4	chr12:51441811..51444855-chr12:51447426..51450145,3	K562	blood:

Variant related genes	Relation type
LETMD1	TF binding region
ENSG00000050426	Chromatin interaction
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1005559	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1038525	0.81[ASN][1000 genomes]
rs1048230	0.87[CEU][hapmap];0.91[GIH][hapmap];0.82[EUR][1000 genomes]
rs10506298	0.82[EUR][1000 genomes]
rs10506299	0.82[EUR][1000 genomes]
rs1056897	0.91[GIH][hapmap];0.81[MEX][hapmap]
rs10747602	0.81[ASN][1000 genomes]
rs10747604	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169633	0.80[EUR][1000 genomes]
rs11169636	0.80[EUR][1000 genomes]
rs11169637	0.80[EUR][1000 genomes]
rs11169641	0.80[EUR][1000 genomes]
rs11169642	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs11169644	0.80[EUR][1000 genomes]
rs11169647	0.80[EUR][1000 genomes]
rs11169648	0.80[EUR][1000 genomes]
rs11169649	0.80[EUR][1000 genomes]
rs11169652	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs11169654	0.87[CEU][hapmap];0.91[GIH][hapmap];0.82[EUR][1000 genomes]
rs11169655	0.82[EUR][1000 genomes]
rs11169661	0.82[EUR][1000 genomes]
rs11169667	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs11169669	0.82[EUR][1000 genomes]
rs11169670	0.82[EUR][1000 genomes]
rs11169671	0.82[EUR][1000 genomes]
rs11169672	0.81[EUR][1000 genomes]
rs11169682	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169712	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169731	0.87[JPT][hapmap]
rs11169752	0.81[GIH][hapmap];0.84[MEX][hapmap]
rs11519977	0.80[EUR][1000 genomes]
rs11738	0.81[GIH][hapmap];0.84[MEX][hapmap]
rs11831810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11831946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11833022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11834746	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12366476	0.80[EUR][1000 genomes]
rs12366756	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs12369639	0.82[CEU][hapmap]
rs12370820	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12371463	0.83[EUR][1000 genomes]
rs12372173	0.85[EUR][1000 genomes]
rs12809563	0.80[EUR][1000 genomes]
rs12809790	0.84[ASN][1000 genomes]
rs12810174	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12810455	0.85[EUR][1000 genomes]
rs12810596	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12810659	0.82[EUR][1000 genomes]
rs12810700	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12810990	0.84[ASN][1000 genomes]
rs12811508	0.81[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs12811658	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12811684	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12812650	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12813309	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12813368	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12813728	0.81[EUR][1000 genomes]
rs12814498	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12817386	0.82[EUR][1000 genomes]
rs12818033	0.80[EUR][1000 genomes]
rs12819225	0.85[EUR][1000 genomes]
rs12819517	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12820074	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12820966	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12821444	0.80[EUR][1000 genomes]
rs12822509	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12823402	0.83[EUR][1000 genomes]
rs12824225	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12824958	0.87[CEU][hapmap];0.88[GIH][hapmap]
rs12826153	0.82[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12827861	0.82[EUR][1000 genomes]
rs12828349	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12828536	0.85[EUR][1000 genomes]
rs12829630	0.85[EUR][1000 genomes]
rs12830048	0.80[EUR][1000 genomes]
rs12830073	0.85[EUR][1000 genomes]
rs12831269	0.82[EUR][1000 genomes]
rs12833314	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12833565	0.85[EUR][1000 genomes]
rs15897	0.82[EUR][1000 genomes]
rs17125137	0.87[CEU][hapmap];0.88[GIH][hapmap];0.80[EUR][1000 genomes]
rs17296192	0.81[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs2285228	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs2285230	0.87[CEU][hapmap];0.91[GIH][hapmap];0.82[EUR][1000 genomes]
rs2301529	0.87[CEU][hapmap];0.91[GIH][hapmap];0.82[EUR][1000 genomes]
rs34057357	0.81[EUR][1000 genomes]
rs34481246	0.85[EUR][1000 genomes]
rs34735738	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35037088	0.80[EUR][1000 genomes]
rs4768964	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768967	0.93[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6580784	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580792	0.81[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.85[EUR][1000 genomes]
rs6580793	0.81[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs67133203	0.84[EUR][1000 genomes]
rs67259551	0.82[EUR][1000 genomes]
rs67260912	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67293043	0.85[EUR][1000 genomes]
rs7135059	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71445772	0.80[EUR][1000 genomes]
rs7305638	0.80[EUR][1000 genomes]
rs7306293	0.80[EUR][1000 genomes]
rs7954140	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7959075	0.80[EUR][1000 genomes]
rs7959082	0.80[EUR][1000 genomes]
rs7960381	0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs7964570	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7972406	0.85[EUR][1000 genomes]
rs7975147	0.85[EUR][1000 genomes]
rs7976777	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7977104	0.91[GIH][hapmap];0.84[MEX][hapmap]
rs7980874	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs970098	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs970099	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51442800-51449000	Weak transcription	Aorta	Aorta
2	chr12:51442800-51449800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:51442800-51450000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:51442800-51452800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:51442800-51470200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:51443000-51453200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:51443200-51449600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:51443400-51449200	Weak transcription	Right Ventricle	heart
9	chr12:51443400-51452600	Weak transcription	Stomach Mucosa	stomach
10	chr12:51443400-51476000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:51443600-51451600	Weak transcription	Colonic Mucosa	Colon
12	chr12:51443600-51451800	Weak transcription	Small Intestine	intestine
13	chr12:51443600-51452600	Weak transcription	Psoas Muscle	Psoas
14	chr12:51443600-51457400	Weak transcription	Fetal Brain Male	brain
15	chr12:51443600-51459600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:51443600-51462800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:51443800-51449000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr12:51443800-51455600	Weak transcription	Fetal Heart	heart
19	chr12:51443800-51462600	Strong transcription	A549	lung
20	chr12:51444000-51449600	Weak transcription	HUVEC	blood vessel
21	chr12:51444200-51452400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:51444200-51454800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr12:51444200-51463200	Strong transcription	Placenta	Placenta
24	chr12:51444200-51465000	Strong transcription	Fetal Muscle Leg	muscle
25	chr12:51444200-51465400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:51444200-51465600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:51444200-51470400	Strong transcription	Fetal Stomach	stomach
28	chr12:51444400-51462800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr12:51444400-51464800	Strong transcription	Fetal Muscle Trunk	muscle
30	chr12:51444600-51455600	Strong transcription	Fetal Intestine Small	intestine
31	chr12:51445000-51467800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr12:51445400-51449600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:51445400-51449800	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr12:51445400-51449800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr12:51445400-51454000	Strong transcription	Left Ventricle	heart
36	chr12:51445400-51462600	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr12:51445400-51462600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr12:51445400-51462600	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr12:51445400-51462800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr12:51445400-51464000	Strong transcription	Fetal Intestine Large	intestine
41	chr12:51445400-51467800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:51445400-51467800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr12:51445400-51469200	Strong transcription	Fetal Thymus	thymus
44	chr12:51445400-51470600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr12:51445600-51449800	Strong transcription	Osteobl	bone
46	chr12:51445600-51450200	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr12:51445600-51450400	Strong transcription	NH-A	brain
48	chr12:51445600-51452400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:51445600-51454200	Strong transcription	Thymus	Thymus
50	chr12:51445600-51456000	Strong transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links