Variant report

Variant	rs12052946
Chromosome Location	chr2:153567946-153567947
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153553988..153556730-chr2:153566964..153569354,3	K562	blood:
2	chr2:153514404..153517682-chr2:153567712..153571488,3	K562	blood:
3	chr2:153537876..153540106-chr2:153567284..153570033,2	K562	blood:
4	chr2:153539766..153542377-chr2:153567671..153570144,2	MCF-7	breast:
5	chr2:153514944..153516806-chr2:153567560..153569212,2	K562	blood:

Variant related genes	Relation type
ENSG00000196504	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10178618	0.90[ASN][1000 genomes]
rs11679491	0.89[ASN][1000 genomes]
rs11883762	0.93[ASN][1000 genomes]
rs13018870	0.90[ASN][1000 genomes]
rs1561267	0.93[ASN][1000 genomes]
rs16831451	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16831529	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831728	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16831736	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2272535	0.90[ASN][1000 genomes]
rs2293680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3748941	0.90[ASN][1000 genomes]
rs3817620	0.93[ASN][1000 genomes]
rs3845678	0.86[ASN][1000 genomes]
rs4146903	0.90[ASN][1000 genomes]
rs4664119	0.90[ASN][1000 genomes]
rs55986999	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6710417	0.93[ASN][1000 genomes]
rs6714218	0.90[ASN][1000 genomes]
rs72858735	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72871129	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72871192	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72872615	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs746780	0.92[ASN][1000 genomes]
rs7592127	0.90[ASN][1000 genomes]
rs893328	0.93[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	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3693438	chr2:153505376-153718246	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153523400-153571800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:153525000-153571800	Weak transcription	Small Intestine	intestine
3	chr2:153533400-153571600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:153533800-153572600	Weak transcription	Fetal Brain Male	brain
5	chr2:153536000-153572600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:153537600-153571800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:153539600-153571800	Weak transcription	Brain Anterior Caudate	brain
8	chr2:153539600-153572400	Weak transcription	Brain Angular Gyrus	brain
9	chr2:153539600-153572400	Weak transcription	Pancreas	Pancrea
10	chr2:153544400-153568200	Weak transcription	Fetal Kidney	kidney
11	chr2:153551200-153568000	Weak transcription	Ovary	ovary
12	chr2:153551200-153571400	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:153551200-153571800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:153551200-153571800	Weak transcription	Brain Substantia Nigra	brain
15	chr2:153551200-153572400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:153551400-153568400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:153551400-153571800	Weak transcription	HSMMtube	muscle
18	chr2:153556800-153568800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:153557200-153570000	Strong transcription	HepG2	liver
20	chr2:153557800-153572200	Strong transcription	Fetal Thymus	thymus
21	chr2:153558200-153573000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:153558600-153572400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:153558600-153572400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:153558600-153572400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:153558600-153572400	Weak transcription	NHLF	lung
26	chr2:153558800-153568400	Weak transcription	Lung	lung
27	chr2:153558800-153571800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:153558800-153571800	Weak transcription	Fetal Intestine Small	intestine
29	chr2:153558800-153572400	Weak transcription	Esophagus	oesophagus
30	chr2:153558800-153573000	Weak transcription	Aorta	Aorta
31	chr2:153558800-153573200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:153558800-153573400	Weak transcription	Spleen	Spleen
33	chr2:153559000-153568200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:153559000-153571200	Weak transcription	Brain Germinal Matrix	brain
35	chr2:153559400-153572400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:153559800-153571400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:153560600-153568400	Weak transcription	Psoas Muscle	Psoas
38	chr2:153560600-153570000	Strong transcription	Primary T cells from cord blood	blood
39	chr2:153560600-153571600	Strong transcription	Fetal Intestine Large	intestine
40	chr2:153561000-153571600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:153561200-153571800	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr2:153561600-153572000	Strong transcription	Duodenum Mucosa	Duodenum
43	chr2:153561800-153570200	Strong transcription	Dnd41	blood
44	chr2:153561800-153571600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:153562000-153571000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:153562000-153572400	Weak transcription	Right Atrium	heart
47	chr2:153562200-153568400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr2:153562200-153571400	Strong transcription	K562	blood
49	chr2:153562600-153571400	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr2:153562600-153571600	Strong transcription	HUES48 Cell Line	embryonic stem cell

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