Variant report

Variant	rs2638335
Chromosome Location	chr12:56880672-56880673
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56862344..56864045-chr12:56880136..56881879,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135517	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10876895	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11171862	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171863	0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171865	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171870	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12304519	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316930	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12809550	0.87[EUR][1000 genomes]
rs12813881	0.84[ASN][1000 genomes]
rs2638285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638318	0.87[EUR][1000 genomes]
rs2638319	0.95[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs2638330	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2638334	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2657909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34287864	0.85[CEU][hapmap]
rs3782235	0.92[LWK][hapmap]
rs3809122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58252713	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6581096	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71459375	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71459376	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7314242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv1052713	chr12:56848036-56917602	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2638335	RBMS2	cis	lymphoblastoid	seeQTL
rs2638335	STAC3	cis	parietal	SCAN
rs2638335	RBMS2	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56863200-56881000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:56863200-56881200	Weak transcription	Ovary	ovary
3	chr12:56863400-56881000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:56863400-56881200	Weak transcription	Right Atrium	heart
5	chr12:56863400-56881400	Weak transcription	HSMMtube	muscle
6	chr12:56863600-56880800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:56863800-56880800	Weak transcription	Brain Germinal Matrix	brain
8	chr12:56863800-56880800	Weak transcription	Gastric	stomach
9	chr12:56863800-56880800	Weak transcription	HMEC	breast
10	chr12:56863800-56881000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:56863800-56881200	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:56863800-56881600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:56864200-56881200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:56864400-56880800	Weak transcription	Lung	lung
15	chr12:56864800-56881000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:56865600-56880800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr12:56865600-56881400	Weak transcription	Aorta	Aorta
18	chr12:56866000-56880800	Weak transcription	Spleen	Spleen
19	chr12:56866000-56881000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:56866000-56881200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:56866200-56881000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr12:56866400-56881000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:56866600-56881200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr12:56866800-56881200	Weak transcription	Primary B cells from cord blood	blood
25	chr12:56867600-56880800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr12:56867600-56880800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:56867600-56881800	Weak transcription	A549	lung
28	chr12:56867800-56881000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr12:56867800-56881000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr12:56867800-56881000	Weak transcription	HSMM	muscle
31	chr12:56868800-56880800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:56868800-56881000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr12:56869000-56881600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:56869400-56880800	Weak transcription	Brain Anterior Caudate	brain
35	chr12:56869400-56881000	Weak transcription	Fetal Heart	heart
36	chr12:56869400-56881000	Weak transcription	Fetal Intestine Large	intestine
37	chr12:56871200-56880800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:56871200-56880800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr12:56871800-56881000	Weak transcription	Brain Hippocampus Middle	brain
40	chr12:56872000-56880800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:56872000-56881200	Weak transcription	Esophagus	oesophagus
42	chr12:56872600-56880800	Weak transcription	Brain Angular Gyrus	brain
43	chr12:56873800-56880800	Weak transcription	Fetal Intestine Small	intestine
44	chr12:56873800-56881000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:56874000-56880800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:56874600-56881000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr12:56874800-56880800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:56874800-56881000	Weak transcription	GM12878-XiMat	blood
49	chr12:56879000-56880800	Enhancers	Pancreas	Pancrea
50	chr12:56879200-56880800	Weak transcription	H9 Cell Line	embryonic stem cell

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