Variant report

Variant	rs2297961
Chromosome Location	chr1:147102157-147102158
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:146964911..146966896-chr1:147101578..147104258,2	MCF-7	breast:
2	chr1:147100097..147104390-chr1:147107931..147112033,4	MCF-7	breast:
3	chr1:146986046..146988556-chr1:147100242..147102169,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10157759	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10793694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11240097	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11240098	1.00[CEU][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11240100	1.00[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11240101	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11240102	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11240103	0.81[ASN][1000 genomes]
rs12025871	1.00[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12028985	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12045199	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12045709	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12046017	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12562949	0.90[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1417279	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1578723	1.00[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1857209	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1857210	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2236571	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2236572	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3766506	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3766507	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3766510	1.00[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3766512	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3818888	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3820126	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3820127	1.00[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41399146	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6663082	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6667707	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6677434	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6681587	0.99[ASN][1000 genomes]
rs72700360	0.82[ASN][1000 genomes]
rs7539714	1.00[CEU][hapmap];0.80[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs867270	0.86[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs870434	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs881085	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs946902	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs946906	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
2	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
3	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
4	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
5	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
6	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
7	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
8	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
9	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
10	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
11	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
12	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
13	nsv872256	chr1:146556596-147410973	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
14	nsv1012331	chr1:146603479-147384720	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
15	nsv535131	chr1:146603479-147384720	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
16	nsv1004849	chr1:146661516-147286826	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
17	nsv535135	chr1:146661516-147286826	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv534063	chr1:146807433-147381411	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
19	nsv1001868	chr1:146893791-147389944	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
20	nsv482606	chr1:146959127-147134517	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
21	nsv872266	chr1:147020099-147381558	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
22	nsv831426	chr1:147089930-147265267	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:147091800-147119800	Weak transcription	Hela-S3	cervix
2	chr1:147092200-147114000	Weak transcription	Fetal Kidney	kidney
3	chr1:147092800-147117600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:147093400-147102400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:147093800-147103800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:147094400-147112400	Weak transcription	Psoas Muscle	Psoas
7	chr1:147095000-147113000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:147096400-147112400	Weak transcription	Placenta	Placenta
9	chr1:147096600-147103600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:147096600-147103800	Weak transcription	Pancreas	Pancrea
11	chr1:147096600-147112800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:147096600-147113400	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:147096600-147115000	Weak transcription	Brain Anterior Caudate	brain
14	chr1:147096600-147115200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:147096600-147122800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:147096800-147102800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:147096800-147103800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:147096800-147112400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:147096800-147112800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:147096800-147112800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:147096800-147112800	Weak transcription	Left Ventricle	heart
22	chr1:147096800-147113400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:147096800-147114200	Weak transcription	Esophagus	oesophagus
24	chr1:147096800-147114200	Weak transcription	Ovary	ovary
25	chr1:147096800-147114400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:147096800-147115000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:147096800-147117000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:147096800-147117200	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:147096800-147119400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:147096800-147119400	Weak transcription	Aorta	Aorta
31	chr1:147096800-147119600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:147096800-147119600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:147096800-147119600	Weak transcription	Gastric	stomach
34	chr1:147096800-147119600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:147096800-147119800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:147097000-147103800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:147097000-147103800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:147097000-147112800	Weak transcription	Right Ventricle	heart
39	chr1:147097000-147113000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:147097000-147114400	Weak transcription	Fetal Brain Female	brain
41	chr1:147097000-147114400	Weak transcription	Thymus	Thymus
42	chr1:147097200-147112800	Weak transcription	NH-A	brain
43	chr1:147097600-147102200	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:147097600-147130000	Weak transcription	Stomach Mucosa	stomach
45	chr1:147097800-147103800	Weak transcription	Fetal Lung	lung
46	chr1:147097800-147106800	Weak transcription	Primary B cells from cord blood	blood
47	chr1:147097800-147111800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:147097800-147112600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr1:147097800-147114600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:147097800-147115000	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links