Variant report

Variant	rs13029949
Chromosome Location	chr2:173988250-173988251
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173959860..173961985-chr2:173986864..173989225,2	MCF-7	breast:
2	chr2:173938392..173941767-chr2:173987528..173992085,5	MCF-7	breast:
3	chr2:173985743..173988657-chr2:173992178..173994964,4	K562	blood:
4	chr2:173987726..173990212-chr8:91575317..91577532,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10930579	0.83[ASN][1000 genomes]
rs12615166	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12986917	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12987496	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12989116	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12990553	0.81[ASN][1000 genomes]
rs12997078	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12998711	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13004212	0.86[ASN][1000 genomes]
rs13017210	0.80[ASN][1000 genomes]
rs13017438	0.83[ASN][1000 genomes]
rs13020796	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13022800	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap]
rs13032010	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs16861278	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs17302977	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17761169	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs2076857	0.88[ASN][1000 genomes]
rs2278883	0.89[ASN][1000 genomes]
rs2289397	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2289399	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs34014656	0.91[ASN][1000 genomes]
rs34472765	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34681024	0.83[ASN][1000 genomes]
rs34702663	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34862313	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35250703	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36102078	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs36103648	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3754741	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs3754743	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3754744	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3769157	0.81[ASN][1000 genomes]
rs3769161	0.88[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs3769167	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs3769187	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3769192	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769194	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3769199	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3769203	0.91[CEU][hapmap];0.89[CHB][hapmap]
rs4972533	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs55913048	0.83[ASN][1000 genomes]
rs56151459	0.89[ASN][1000 genomes]
rs56193548	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56342397	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6433395	0.84[CEU][hapmap];0.90[CHB][hapmap]
rs71417423	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72905080	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv834461	chr2:173979734-174038471	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173945400-173991200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:173953800-173991400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:173965400-173989200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:173968600-173990600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:173974400-174005200	Weak transcription	Fetal Intestine Small	intestine
6	chr2:173974800-173988600	Weak transcription	HSMM	muscle
7	chr2:173974800-173991400	Weak transcription	K562	blood
8	chr2:173978200-173995200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:173980600-173989200	Weak transcription	Esophagus	oesophagus
10	chr2:173981000-174000800	Weak transcription	Fetal Thymus	thymus
11	chr2:173982800-174006400	Weak transcription	Fetal Lung	lung
12	chr2:173984200-174000200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:173984400-173989000	Weak transcription	Lung	lung
14	chr2:173984400-173989000	Weak transcription	Right Atrium	heart
15	chr2:173984400-173994200	Weak transcription	Gastric	stomach
16	chr2:173984400-173994600	Weak transcription	Pancreas	Pancrea
17	chr2:173984600-173989000	Weak transcription	Aorta	Aorta
18	chr2:173984600-173994800	Weak transcription	Liver	Liver
19	chr2:173984600-173995400	Weak transcription	Fetal Stomach	stomach
20	chr2:173984800-173991400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:173985000-173988600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:173985000-173989200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:173985200-173995400	Weak transcription	Adipose Nuclei	Adipose
24	chr2:173985400-173988600	Weak transcription	Primary B cells from cord blood	blood
25	chr2:173985400-173995400	Weak transcription	Ovary	ovary
26	chr2:173985800-173989200	Weak transcription	NH-A	brain
27	chr2:173985800-173989800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:173986000-173988400	Enhancers	Right Ventricle	heart
29	chr2:173986000-173989000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:173986000-173989000	Weak transcription	NHLF	lung
31	chr2:173986000-173995000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr2:173986200-173988400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:173986200-173989000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:173986200-173989800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr2:173986200-173997200	Weak transcription	Fetal Muscle Leg	muscle
36	chr2:173986800-173989000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:173986800-173990000	Enhancers	Fetal Heart	heart
38	chr2:173986800-173995200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:173987000-173990200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr2:173987200-173989800	Enhancers	Osteobl	bone
41	chr2:173987200-173990200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:173987200-173990200	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr2:173987400-173988400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:173987400-173988600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:173987400-173990400	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr2:173987600-173988600	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr2:173987600-173990200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:173987600-173992000	Enhancers	HMEC	breast
49	chr2:173987800-173989400	Enhancers	NHEK	skin
50	chr2:173987800-173989600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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