Variant report

Variant	rs2496139
Chromosome Location	chr6:13375136-13375137
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13374146..13377100-chr6:13377431..13379906,2	MCF-7	breast:
2	chr6:13374615..13376910-chr6:13377833..13379393,2	K562	blood:
3	chr6:13370869..13372385-chr6:13372933..13375526,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10807431	0.85[EUR][1000 genomes]
rs10807432	0.81[EUR][1000 genomes]
rs10948650	0.92[EUR][1000 genomes]
rs12153966	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439536	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2496160	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2496161	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2496162	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2496173	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28813108	0.82[EUR][1000 genomes]
rs4711978	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs474159	0.83[EUR][1000 genomes]
rs476904	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs489396	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs491278	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs492433	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs501987	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs510932	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs516003	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs517803	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs524118	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs531256	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs548119	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs552655	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs553671	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs553948	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs560396	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs564174	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs570315	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs573109	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs575709	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs579028	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7760579	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs821276	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs821277	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9357708	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9367440	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13355600-13383400	Weak transcription	A549	lung
2	chr6:13356200-13378200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:13361600-13378200	Weak transcription	Fetal Thymus	thymus
4	chr6:13365000-13377800	Weak transcription	Primary B cells from cord blood	blood
5	chr6:13365400-13379800	Weak transcription	Primary T cells from cord blood	blood
6	chr6:13365600-13378000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:13365800-13377600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr6:13365800-13378800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:13365800-13378800	Weak transcription	Gastric	stomach
10	chr6:13365800-13379400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:13365800-13379600	Weak transcription	Brain Germinal Matrix	brain
12	chr6:13365800-13380600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:13365800-13385400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:13366000-13378200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:13366000-13378200	Weak transcription	Colonic Mucosa	Colon
16	chr6:13366000-13378600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:13366000-13380600	Weak transcription	Ovary	ovary
18	chr6:13366000-13382800	Weak transcription	Liver	Liver
19	chr6:13366000-13386800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:13368000-13404600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:13368200-13381000	Weak transcription	NH-A	brain
22	chr6:13368400-13375800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:13368400-13386600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:13368600-13375600	Weak transcription	Esophagus	oesophagus
25	chr6:13368600-13377600	Weak transcription	Aorta	Aorta
26	chr6:13368800-13375400	Weak transcription	Psoas Muscle	Psoas
27	chr6:13371600-13375400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:13371800-13375200	Weak transcription	NHEK	skin
29	chr6:13371800-13375400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:13371800-13375600	Weak transcription	HMEC	breast
31	chr6:13372200-13375400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:13372200-13380600	Weak transcription	Lung	lung
33	chr6:13372400-13381000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr6:13372800-13379000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:13372800-13380600	Weak transcription	Fetal Brain Female	brain
36	chr6:13372800-13380800	Weak transcription	Fetal Brain Male	brain
37	chr6:13373000-13377400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr6:13373000-13379200	Weak transcription	Brain Angular Gyrus	brain
39	chr6:13373000-13379200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr6:13373200-13375800	Weak transcription	Left Ventricle	heart
41	chr6:13373200-13378800	Weak transcription	Right Atrium	heart
42	chr6:13373400-13375400	Weak transcription	Spleen	Spleen
43	chr6:13373400-13376600	Weak transcription	Right Ventricle	heart
44	chr6:13373600-13379400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:13373800-13375200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr6:13374200-13378400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:13374200-13379200	Weak transcription	Brain Substantia Nigra	brain
48	chr6:13374200-13380800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:13374400-13375400	Weak transcription	Adipose Nuclei	Adipose
50	chr6:13374400-13375400	Enhancers	GM12878-XiMat	blood

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