Variant report

Variant	rs12329205
Chromosome Location	chr2:38789508-38789509
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38788213..38790440-chr2:38791482..38793499,2	MCF-7	breast:
2	chr2:38788017..38790362-chr2:38797831..38799646,2	K562	blood:
3	chr2:38786392..38790076-chr2:38975715..38979796,3	MCF-7	breast:
4	chr2:38788831..38791185-chr2:38805225..38808104,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HNRPLL-4	chr2:38787215-38789656	NONHSAT070189

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12105070	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12622497	0.84[JPT][hapmap]
rs12712608	0.90[ASN][1000 genomes]
rs13431551	0.81[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[ASN][1000 genomes]
rs1368114	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.97[ASN][1000 genomes]
rs1579537	0.81[CEU][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs17022904	0.86[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17022996	0.83[JPT][hapmap];0.89[YRI][hapmap]
rs17023003	0.81[CHD][hapmap]
rs2116385	0.83[JPT][hapmap]
rs2253519	0.81[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2373421	0.83[JPT][hapmap]
rs2373423	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731841	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6544169	0.81[CEU][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap]
rs6721860	0.87[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap]
rs6727476	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6733950	0.87[CHD][hapmap];0.83[GIH][hapmap]
rs6736320	0.94[ASN][1000 genomes]
rs6742843	0.83[JPT][hapmap]
rs6757844	0.81[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap]
rs7571463	0.90[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.83[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12329205	CRIM1	cis	parietal	SCAN
rs12329205	QPCT	cis	parietal	SCAN
rs12329205	MAMSTR	trans	parietal	SCAN

Chromatin state (count:119 , 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	chr2:38768400-38791600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:38769000-38793200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:38770400-38791000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr2:38770400-38794600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:38770600-38794800	Weak transcription	NHEK	skin
8	chr2:38770800-38794400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:38775800-38821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:38776600-38791000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:38777000-38794600	Weak transcription	Brain Anterior Caudate	brain
12	chr2:38777000-38807200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:38777200-38794200	Weak transcription	Ovary	ovary
14	chr2:38777400-38792600	Weak transcription	Thymus	Thymus
15	chr2:38778200-38791400	Weak transcription	Fetal Intestine Small	intestine
16	chr2:38778200-38794200	Weak transcription	Lung	lung
17	chr2:38779000-38791400	Weak transcription	Fetal Stomach	stomach
18	chr2:38779000-38818200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:38779400-38794800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:38779400-38821800	Weak transcription	Right Ventricle	heart
21	chr2:38779600-38793600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:38779600-38807400	Weak transcription	Fetal Heart	heart
23	chr2:38779600-38812800	Weak transcription	Aorta	Aorta
24	chr2:38779800-38800200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr2:38780200-38794600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:38780200-38794800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr2:38780400-38791200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:38780400-38797200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr2:38780600-38792600	Weak transcription	K562	blood
30	chr2:38781200-38827600	Weak transcription	Esophagus	oesophagus
31	chr2:38781400-38794600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:38781600-38797600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:38782000-38794600	Weak transcription	Gastric	stomach
34	chr2:38782400-38819000	Strong transcription	Fetal Thymus	thymus
35	chr2:38782600-38795400	Weak transcription	Brain Angular Gyrus	brain
36	chr2:38782800-38799000	Strong transcription	HSMM	muscle
37	chr2:38783600-38792600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:38783600-38794200	Weak transcription	Fetal Brain Female	brain
39	chr2:38783600-38797600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:38783800-38794600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:38783800-38827800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:38784600-38791400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:38784600-38793600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:38784800-38794600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:38785000-38827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr2:38785400-38801400	Weak transcription	GM12878-XiMat	blood
47	chr2:38785800-38791200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:38786000-38794600	Weak transcription	Pancreas	Pancrea
49	chr2:38786000-38827600	Weak transcription	Colonic Mucosa	Colon
50	chr2:38786200-38789600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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