Variant report

Variant	rs870799
Chromosome Location	chr12:64191396-64191397
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64172589..64175160-chr12:64189373..64193026,5	MCF-7	breast:
2	chr12:64180929..64182540-chr12:64189836..64191999,2	MCF-7	breast:
3	chr12:64189848..64191605-chr12:64194273..64195833,2	MCF-7	breast:
4	chr12:64172671..64176292-chr12:64191216..64196632,5	MCF-7	breast:
5	chr12:64177549..64179477-chr12:64189531..64192221,2	K562	blood:

Variant related genes	Relation type
ENSG00000118600	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11175159	1.00[CEU][hapmap]
rs11175161	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs11175166	0.80[EUR][1000 genomes]
rs12227489	1.00[CEU][hapmap]
rs12228388	1.00[CEU][hapmap]
rs12230610	1.00[CEU][hapmap]
rs12582841	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2336002	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4762999	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763000	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763115	0.85[JPT][hapmap]
rs4763121	1.00[CEU][hapmap]
rs58158451	0.80[EUR][1000 genomes]
rs59554455	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60631306	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61440913	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73311798	0.80[EUR][1000 genomes]
rs931911	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2759905	chr12:63901801-64252172	Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758312	chr12:63910416-64252172	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv899171	chr12:63916682-64202233	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2751110	chr12:63939733-64274680	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv832441	chr12:64063776-64252172	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv3485882	chr12:64178755-64196017	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3485883	chr12:64178755-64196017	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv3488108	chr12:64178778-64195988	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv3488119	chr12:64178778-64195988	Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv746	chr12:64189444-64234966	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64174400-64200200	Weak transcription	Spleen	Spleen
2	chr12:64174400-64201800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:64174400-64203400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:64174400-64204400	Weak transcription	Small Intestine	intestine
5	chr12:64174400-64204800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:64174600-64199400	Weak transcription	Brain Substantia Nigra	brain
7	chr12:64174600-64200200	Weak transcription	HSMMtube	muscle
8	chr12:64174600-64200600	Weak transcription	Thymus	Thymus
9	chr12:64174600-64201000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:64174600-64204400	Weak transcription	Colonic Mucosa	Colon
11	chr12:64174800-64199200	Weak transcription	Stomach Mucosa	stomach
12	chr12:64174800-64208000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:64174800-64208000	Weak transcription	Fetal Brain Male	brain
14	chr12:64174800-64208600	Weak transcription	Fetal Brain Female	brain
15	chr12:64175000-64200200	Weak transcription	Brain Anterior Caudate	brain
16	chr12:64175200-64199400	Weak transcription	NHLF	lung
17	chr12:64175200-64202400	Weak transcription	Fetal Heart	heart
18	chr12:64175200-64205200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:64175400-64200800	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:64175400-64201800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr12:64175400-64202600	Weak transcription	Hela-S3	cervix
22	chr12:64175400-64202800	Weak transcription	HUVEC	blood vessel
23	chr12:64175400-64204400	Weak transcription	Brain Angular Gyrus	brain
24	chr12:64175600-64208000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:64178000-64209800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr12:64178400-64204000	Weak transcription	HMEC	breast
27	chr12:64178600-64208400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr12:64178800-64201600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:64181000-64200600	Weak transcription	Gastric	stomach
30	chr12:64181000-64204400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:64181200-64204400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:64181200-64205400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr12:64181800-64201000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:64181800-64201600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:64182000-64208000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr12:64182800-64205200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:64183000-64198200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:64183400-64199000	Weak transcription	Fetal Muscle Leg	muscle
39	chr12:64184200-64199200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr12:64184200-64202000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr12:64184400-64199200	Weak transcription	Fetal Thymus	thymus
42	chr12:64184400-64199200	Weak transcription	GM12878-XiMat	blood
43	chr12:64184400-64199200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr12:64184400-64203600	Weak transcription	K562	blood
45	chr12:64184400-64204200	Weak transcription	NHEK	skin
46	chr12:64184600-64199600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr12:64184600-64200600	Weak transcription	Lung	lung
48	chr12:64184600-64202000	Weak transcription	Fetal Intestine Large	intestine
49	chr12:64184600-64204400	Weak transcription	Esophagus	oesophagus
50	chr12:64184600-64205800	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links