Variant report

Variant	rs17576044
Chromosome Location	chr2:38788315-38788316
allele	A/G
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	chr2:38781921..38784416-chr2:38785346..38789078,4	K562	blood:

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

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12614876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs12616367	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12619629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12621788	0.83[EUR][1000 genomes]
rs1543881	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17022945	0.81[YRI][hapmap]
rs17603782	1.00[CEU][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34133986	1.00[EUR][1000 genomes]
rs36024292	1.00[EUR][1000 genomes]
rs3765001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs41446253	0.81[YRI][hapmap]
rs55785223	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55833813	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56956410	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6544165	1.00[CEU][hapmap]
rs6710613	0.89[YRI][hapmap]
rs6732743	0.87[YRI][hapmap]
rs6754893	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6760965	1.00[CEU][hapmap]
rs72895897	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72905831	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72905839	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73929040	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73929052	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7578356	1.00[CHB][hapmap]
rs7579783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs7580657	0.83[AMR][1000 genomes]
rs7584862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606515	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[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:118 , 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	chr2:38769200-38788400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:38770000-38788600	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:38770400-38791000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr2:38770400-38794600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:38770600-38794800	Weak transcription	NHEK	skin
10	chr2:38770800-38794400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:38775800-38821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:38776600-38791000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:38776800-38788800	Weak transcription	Fetal Brain Male	brain
14	chr2:38777000-38794600	Weak transcription	Brain Anterior Caudate	brain
15	chr2:38777000-38807200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:38777200-38794200	Weak transcription	Ovary	ovary
17	chr2:38777400-38792600	Weak transcription	Thymus	Thymus
18	chr2:38778200-38791400	Weak transcription	Fetal Intestine Small	intestine
19	chr2:38778200-38794200	Weak transcription	Lung	lung
20	chr2:38779000-38791400	Weak transcription	Fetal Stomach	stomach
21	chr2:38779000-38818200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:38779400-38794800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:38779400-38821800	Weak transcription	Right Ventricle	heart
24	chr2:38779600-38793600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:38779600-38807400	Weak transcription	Fetal Heart	heart
26	chr2:38779600-38812800	Weak transcription	Aorta	Aorta
27	chr2:38779800-38800200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr2:38780200-38794600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:38780200-38794800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr2:38780400-38791200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:38780400-38797200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr2:38780600-38792600	Weak transcription	K562	blood
33	chr2:38781200-38827600	Weak transcription	Esophagus	oesophagus
34	chr2:38781400-38794600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:38781600-38797600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:38782000-38794600	Weak transcription	Gastric	stomach
37	chr2:38782400-38819000	Strong transcription	Fetal Thymus	thymus
38	chr2:38782600-38795400	Weak transcription	Brain Angular Gyrus	brain
39	chr2:38782800-38799000	Strong transcription	HSMM	muscle
40	chr2:38783600-38792600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:38783600-38794200	Weak transcription	Fetal Brain Female	brain
42	chr2:38783600-38797600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:38783800-38794600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr2:38783800-38827800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:38784600-38791400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:38784600-38793600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr2:38784800-38794600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:38785000-38827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr2:38785200-38788600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:38785400-38801400	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links