Variant report

Variant	rs10875990
Chromosome Location	chr12:50372026-50372027
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50366078..50367703-chr12:50370962..50372946,2	K562	blood:
2	chr12:50342580..50344852-chr12:50371020..50373732,2	MCF-7	breast:
3	chr12:50368103..50369610-chr12:50371234..50372946,2	K562	blood:
4	chr12:50359065..50361531-chr12:50371208..50373985,2	K562	blood:
5	chr12:50368076..50369916-chr12:50370500..50372771,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000086159	Chromatin interaction
ENSG00000167580	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11169232	0.95[ASN][1000 genomes]
rs17124264	0.90[GIH][hapmap]
rs2291612	0.90[GIH][hapmap]
rs55810714	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs629754	0.90[GIH][hapmap]
rs7131715	0.90[GIH][hapmap]
rs7303531	0.90[GIH][hapmap]
rs7309966	0.90[GIH][hapmap]

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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv899072	chr12:50326176-50379667	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	esv1827130	chr12:50349765-50379667	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS 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	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50361400-50372800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:50362600-50385800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:50366400-50374600	Weak transcription	Fetal Kidney	kidney
4	chr12:50366600-50377400	Weak transcription	NHEK	skin
5	chr12:50367000-50378000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:50367400-50401200	Weak transcription	Gastric	stomach
7	chr12:50367600-50374800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:50368400-50374600	Weak transcription	Pancreas	Pancrea
9	chr12:50368400-50376000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:50368600-50372800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:50368800-50373600	Weak transcription	GM12878-XiMat	blood
12	chr12:50369000-50372400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:50369200-50372400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:50369200-50374200	Weak transcription	Liver	Liver
15	chr12:50369200-50374600	Weak transcription	HSMMtube	muscle
16	chr12:50369200-50376000	Weak transcription	Fetal Lung	lung
17	chr12:50369200-50377400	Weak transcription	Right Ventricle	heart
18	chr12:50369200-50377600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:50369200-50381600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:50369400-50372600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr12:50369400-50377600	Weak transcription	Fetal Thymus	thymus
22	chr12:50369600-50372200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:50369600-50372400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr12:50369600-50372600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:50369600-50372800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:50369600-50377400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:50369600-50377400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:50369600-50379200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr12:50369600-50418200	Weak transcription	Colonic Mucosa	Colon
30	chr12:50369800-50372600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:50369800-50373200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:50369800-50376000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:50370000-50375200	Weak transcription	Colon Smooth Muscle	Colon
34	chr12:50370000-50377800	Weak transcription	Thymus	Thymus
35	chr12:50370200-50376000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:50370600-50372800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr12:50370800-50372200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:50371000-50373400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr12:50371400-50372800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:50371600-50375400	Enhancers	Fetal Stomach	stomach
41	chr12:50371800-50372800	Enhancers	Brain Anterior Caudate	brain
42	chr12:50371800-50372800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr12:50371800-50372800	Enhancers	Fetal Intestine Small	intestine
44	chr12:50371800-50375000	Enhancers	Fetal Brain Female	brain
45	chr12:50371800-50376000	Weak transcription	Fetal Intestine Large	intestine
46	chr12:50372000-50372200	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr12:50372000-50372200	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr12:50372000-50372400	Enhancers	Spleen	Spleen
49	chr12:50372000-50372600	Enhancers	Brain Hippocampus Middle	brain
50	chr12:50372000-50372600	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links