Variant report

Variant	rs12712608
Chromosome Location	chr2:38786918-38786919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38779577..38781346-chr2:38785397..38787246,2	K562	blood:
2	chr2:38786011..38787740-chr2:38976954..38979344,3	K562	blood:
3	chr2:38783818..38787523-chr2:38967718..38971056,4	K562	blood:
4	chr2:38786392..38790076-chr2:38975715..38979796,3	MCF-7	breast:
5	chr2:38781921..38784416-chr2:38785346..38789078,4	K562	blood:

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12105070	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12329205	0.90[ASN][1000 genomes]
rs13431551	0.84[ASN][1000 genomes]
rs1368114	0.87[ASN][1000 genomes]
rs1579537	0.80[ASN][1000 genomes]
rs17022904	0.80[ASN][1000 genomes]
rs2253519	0.83[ASN][1000 genomes]
rs2373423	0.90[ASN][1000 genomes]
rs34092964	0.84[ASN][1000 genomes]
rs3731841	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6736320	0.84[ASN][1000 genomes]
rs7571463	0.87[ASN][1000 genomes]
rs7584547	0.80[EUR][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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv1796304	chr2:38766721-38790750	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38763600-38809600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:38768200-38812800	Weak transcription	Psoas Muscle	Psoas
3	chr2:38768400-38787800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:38768400-38788000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:38768400-38791600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:38769000-38793200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:38769200-38787800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:38769200-38788400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:38770000-38788600	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:38770400-38787200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:38770400-38787200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:38770400-38787200	Weak transcription	Fetal Intestine Large	intestine
13	chr2:38770400-38787200	Weak transcription	NHLF	lung
14	chr2:38770400-38787200	Weak transcription	Osteobl	bone
15	chr2:38770400-38787400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:38770400-38787400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:38770400-38791000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:38770400-38794600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:38770600-38787400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:38770600-38794800	Weak transcription	NHEK	skin
21	chr2:38770800-38794400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:38771200-38787200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:38771200-38787400	Weak transcription	HUVEC	blood vessel
24	chr2:38772800-38787400	Weak transcription	HepG2	liver
25	chr2:38775800-38821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:38776400-38787400	Weak transcription	Fetal Kidney	kidney
27	chr2:38776600-38787200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:38776600-38787400	Weak transcription	Placenta	Placenta
29	chr2:38776600-38788000	Weak transcription	Brain Germinal Matrix	brain
30	chr2:38776600-38791000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:38776800-38787200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:38776800-38787200	Weak transcription	Fetal Lung	lung
33	chr2:38776800-38787400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:38776800-38788800	Weak transcription	Fetal Brain Male	brain
35	chr2:38777000-38787200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr2:38777000-38794600	Weak transcription	Brain Anterior Caudate	brain
37	chr2:38777000-38807200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr2:38777200-38787200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr2:38777200-38794200	Weak transcription	Ovary	ovary
40	chr2:38777400-38792600	Weak transcription	Thymus	Thymus
41	chr2:38777600-38787200	Weak transcription	A549	lung
42	chr2:38777600-38787400	Weak transcription	HMEC	breast
43	chr2:38778200-38787200	Weak transcription	Left Ventricle	heart
44	chr2:38778200-38791400	Weak transcription	Fetal Intestine Small	intestine
45	chr2:38778200-38794200	Weak transcription	Lung	lung
46	chr2:38778600-38787200	Weak transcription	Fetal Muscle Leg	muscle
47	chr2:38779000-38791400	Weak transcription	Fetal Stomach	stomach
48	chr2:38779000-38818200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:38779400-38794800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr2:38779400-38821800	Weak transcription	Right Ventricle	heart

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