Variant report

Variant	rs12105827
Chromosome Location	chr2:38771159-38771160
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38751112..38753312-chr2:38768692..38771301,2	K562	blood:
2	chr2:38769946..38771644-chr2:38978190..38979713,2	MCF-7	breast:
3	chr2:38695942..38698846-chr2:38770341..38773070,2	K562	blood:
4	chr2:38770232..38774244-chr2:38976034..38979615,5	K562	blood:
5	chr2:38767755..38769303-chr2:38769457..38771424,2	K562	blood:

Variant related genes	Relation type
ENSG00000231367	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12993657	0.90[ASN][1000 genomes]
rs13003268	0.89[ASN][1000 genomes]
rs13008970	0.91[ASN][1000 genomes]
rs13011825	0.90[ASN][1000 genomes]
rs13017981	0.91[ASN][1000 genomes]
rs17421378	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17421399	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17493321	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17493363	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17493370	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17493538	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17493594	0.89[EUR][1000 genomes]
rs1864828	0.89[EUR][1000 genomes]
rs34171322	0.83[ASN][1000 genomes]
rs34218951	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34311924	0.90[ASN][1000 genomes]
rs34355269	0.87[ASN][1000 genomes]
rs34655983	0.93[ASN][1000 genomes]
rs35066504	0.90[ASN][1000 genomes]
rs35120096	0.89[ASN][1000 genomes]
rs35275207	0.89[ASN][1000 genomes]
rs35299812	0.82[ASN][1000 genomes]
rs35704960	0.93[ASN][1000 genomes]
rs35789272	0.93[ASN][1000 genomes]
rs35803605	0.83[ASN][1000 genomes]
rs3731843	0.89[ASN][1000 genomes]
rs56217714	0.88[EUR][1000 genomes]
rs56311849	0.82[EUR][1000 genomes]
rs6544170	0.90[EUR][1000 genomes]
rs6745023	0.88[EUR][1000 genomes]
rs72795132	0.90[ASN][1000 genomes]
rs7571463	0.85[EUR][1000 genomes]
rs7573095	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7574556	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7584009	0.83[ASN][1000 genomes]
rs7592090	0.90[ASN][1000 genomes]
rs7603200	0.89[ASN][1000 genomes]
rs7606253	0.90[ASN][1000 genomes]
rs7606376	0.90[ASN][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:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38763600-38809600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:38763800-38778800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:38767400-38773400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:38767800-38771200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr2:38768200-38812800	Weak transcription	Psoas Muscle	Psoas
6	chr2:38768400-38771200	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr2:38768400-38787800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:38768400-38788000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr2:38768400-38791600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:38768800-38779000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:38769000-38771200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr2:38769000-38793200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:38769200-38776800	Weak transcription	Brain Anterior Caudate	brain
14	chr2:38769200-38782800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr2:38769200-38787800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:38769200-38788400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:38769600-38775600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:38769600-38777000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:38769800-38771200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:38770000-38771200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr2:38770000-38788600	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:38770200-38771400	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr2:38770200-38771400	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr2:38770200-38777600	Weak transcription	HSMM	muscle
25	chr2:38770200-38781000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:38770400-38771200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:38770400-38771200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:38770400-38772200	Enhancers	Dnd41	blood
29	chr2:38770400-38772800	Enhancers	HepG2	liver
30	chr2:38770400-38776200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:38770400-38776200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr2:38770400-38776400	Weak transcription	Ovary	ovary
33	chr2:38770400-38778400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:38770400-38778800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:38770400-38778800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:38770400-38778800	Weak transcription	HSMMtube	muscle
37	chr2:38770400-38786600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:38770400-38787200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:38770400-38787200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr2:38770400-38787200	Weak transcription	Fetal Intestine Large	intestine
41	chr2:38770400-38787200	Weak transcription	NHLF	lung
42	chr2:38770400-38787200	Weak transcription	Osteobl	bone
43	chr2:38770400-38787400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:38770400-38787400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:38770400-38791000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr2:38770400-38794600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr2:38770600-38771200	Enhancers	Hela-S3	cervix
48	chr2:38770600-38771200	Enhancers	HUVEC	blood vessel
49	chr2:38770600-38775000	Weak transcription	A549	lung
50	chr2:38770600-38776000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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