Variant report

Variant	rs4907258
Chromosome Location	chr2:97554706-97554707
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97537902..97538859-chr2:97554150..97554802,2	MCF-7	breast:
2	chr2:97547842..97556078-chr2:97610100..97619985,30	MCF-7	breast:
3	chr2:74209535..74211828-chr2:97552282..97555129,2	MCF-7	breast:
4	chr2:97523903..97524531-chr2:97554522..97555349,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168754	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10169387	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182668	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs10182965	0.90[ASW][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs11677797	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11694296	0.90[ASW][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs12613171	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs13383845	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13410790	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13421275	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13423092	1.00[ASW][hapmap];1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13425281	0.90[ASW][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2314650	0.92[AMR][1000 genomes]
rs28687044	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4907203	1.00[ASW][hapmap];1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4907204	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4907205	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4907206	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4907256	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[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]
rs4907257	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[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]
rs4907259	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4907260	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61382911	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97536800-97555200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:97542800-97557400	Enhancers	Placenta	Placenta
3	chr2:97546000-97555000	Enhancers	Placenta Amnion	Placenta Amnion
4	chr2:97547800-97555000	Enhancers	Esophagus	oesophagus
5	chr2:97548200-97555400	Enhancers	Fetal Muscle Leg	muscle
6	chr2:97548600-97556000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:97550400-97555000	Enhancers	Fetal Stomach	stomach
8	chr2:97550600-97554800	Enhancers	Fetal Lung	lung
9	chr2:97550800-97555000	Enhancers	Brain Anterior Caudate	brain
10	chr2:97551000-97555000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:97551200-97555000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:97551600-97555000	Enhancers	Colonic Mucosa	Colon
13	chr2:97551800-97554800	Enhancers	NHEK	skin
14	chr2:97551800-97555000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:97551800-97555000	Enhancers	Lung	lung
16	chr2:97552000-97554800	Enhancers	Right Atrium	heart
17	chr2:97552000-97556600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr2:97552000-97556800	Weak transcription	Liver	Liver
19	chr2:97552200-97554800	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr2:97552200-97557000	Weak transcription	A549	lung
21	chr2:97552400-97554800	Enhancers	HSMMtube	muscle
22	chr2:97552400-97555200	Enhancers	Fetal Muscle Trunk	muscle
23	chr2:97552600-97560800	Weak transcription	Hela-S3	cervix
24	chr2:97552800-97555000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr2:97553000-97554800	Enhancers	Fetal Intestine Large	intestine
26	chr2:97553000-97554800	Enhancers	Right Ventricle	heart
27	chr2:97553000-97554800	Enhancers	Stomach Mucosa	stomach
28	chr2:97553000-97554800	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr2:97553000-97555000	Enhancers	Primary B cells from peripheral blood	blood
30	chr2:97553000-97555000	Enhancers	Duodenum Mucosa	Duodenum
31	chr2:97553000-97555000	Enhancers	Fetal Intestine Small	intestine
32	chr2:97553000-97555000	Enhancers	HSMM	muscle
33	chr2:97553200-97554800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:97553200-97554800	Enhancers	Fetal Thymus	thymus
35	chr2:97553200-97555000	Enhancers	Pancreas	Pancrea
36	chr2:97553400-97554800	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr2:97553400-97555000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:97553400-97555000	Enhancers	Brain Substantia Nigra	brain
39	chr2:97553400-97555000	Enhancers	Spleen	Spleen
40	chr2:97553400-97556000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:97553400-97556200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:97553600-97554800	Enhancers	Fetal Brain Female	brain
43	chr2:97553600-97555000	Enhancers	Primary T cells fromperipheralblood	blood
44	chr2:97553600-97555000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr2:97553800-97554800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:97553800-97554800	Enhancers	Psoas Muscle	Psoas
47	chr2:97553800-97555000	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr2:97553800-97555400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr2:97554000-97555000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:97554000-97555000	Enhancers	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links