Variant report

Variant	rs6755640
Chromosome Location	chr2:99445917-99445918
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99434724..99436246-chr2:99444476..99446332,2	MCF-7	breast:
2	chr2:99437609..99439814-chr2:99443387..99445956,2	MCF-7	breast:
3	chr2:99443633..99446031-chr2:99448768..99450507,2	K562	blood:
4	chr2:99344971..99347100-chr2:99444571..99447459,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196872	Chromatin interaction
ENSG00000071073	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10174531	0.89[ASN][1000 genomes]
rs10175560	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10182043	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10202643	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123754	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11123756	0.80[EUR][1000 genomes]
rs11900176	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11900524	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12478574	0.81[EUR][1000 genomes]
rs12712033	0.80[EUR][1000 genomes]
rs12712034	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12712037	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12990579	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13005148	0.83[EUR][1000 genomes]
rs1962029	0.80[EUR][1000 genomes]
rs2276604	0.83[EUR][1000 genomes]
rs2280142	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35929117	0.80[EUR][1000 genomes]
rs4499468	0.81[EUR][1000 genomes]
rs4553869	0.80[EUR][1000 genomes]
rs6542837	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6704682	0.80[EUR][1000 genomes]
rs6714330	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6739097	0.84[EUR][1000 genomes]
rs6753465	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6753879	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6757098	0.81[EUR][1000 genomes]
rs6760065	0.81[EUR][1000 genomes]
rs73962464	0.88[ASN][1000 genomes]
rs7560696	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7565510	0.80[EUR][1000 genomes]
rs7565614	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7565736	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7590596	0.83[EUR][1000 genomes]
rs883773	0.80[EUR][1000 genomes]
rs885115	1.00[AMR][1000 genomes];1.00[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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582517	chr2:99440917-99487972	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99438800-99448600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr2:99439800-99446200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:99439800-99448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:99440000-99447600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:99440000-99460600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:99440200-99449800	Weak transcription	Colonic Mucosa	Colon
7	chr2:99440400-99453800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:99440400-99463400	Weak transcription	Fetal Intestine Large	intestine
9	chr2:99440600-99449600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:99440600-99449600	Weak transcription	HMEC	breast
11	chr2:99440600-99453800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:99441000-99449600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:99441800-99446600	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr2:99441800-99449000	Weak transcription	Brain Anterior Caudate	brain
15	chr2:99442600-99449800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr2:99443000-99448600	Weak transcription	Brain Angular Gyrus	brain
17	chr2:99443000-99448600	Weak transcription	Right Ventricle	heart
18	chr2:99443600-99450400	Weak transcription	Pancreas	Pancrea
19	chr2:99443800-99447800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr2:99443800-99448600	Weak transcription	Esophagus	oesophagus
21	chr2:99443800-99449600	Weak transcription	Gastric	stomach
22	chr2:99444000-99446600	Enhancers	Primary T cells fromperipheralblood	blood
23	chr2:99444000-99447400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:99444200-99446400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr2:99444200-99446400	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr2:99444200-99446800	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr2:99444200-99446800	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr2:99444200-99447000	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr2:99444200-99447600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr2:99444200-99448000	Enhancers	Fetal Thymus	thymus
31	chr2:99444200-99450800	Enhancers	HepG2	liver
32	chr2:99444200-99451000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:99444400-99446600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr2:99444400-99446800	Enhancers	Primary T cells from cord blood	blood
35	chr2:99444400-99447200	Weak transcription	Fetal Intestine Small	intestine
36	chr2:99444400-99447800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:99444600-99446400	Enhancers	Hela-S3	cervix
38	chr2:99444600-99446600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:99444600-99446800	Enhancers	Primary hematopoietic stem cells	blood
40	chr2:99444800-99446600	Enhancers	Duodenum Mucosa	Duodenum
41	chr2:99445000-99446600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:99445200-99446400	Enhancers	Thymus	Thymus
43	chr2:99445200-99447000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr2:99445200-99447000	Enhancers	HUVEC	blood vessel
45	chr2:99445400-99450000	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr2:99445600-99446000	Bivalent Enhancer	Adipose Nuclei	Adipose
47	chr2:99445600-99446000	Enhancers	Right Atrium	heart
48	chr2:99445600-99446000	Enhancers	Stomach Mucosa	stomach
49	chr2:99445600-99446000	Enhancers	Spleen	Spleen
50	chr2:99445600-99446000	Flanking Active TSS	Dnd41	blood

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