Variant report

Variant	rs333996
Chromosome Location	chr2:179108299-179108300
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179078656..179081622-chr2:179106356..179108991,2	K562	blood:
2	chr2:179103455..179105342-chr2:179107240..179109495,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10197166	0.87[JPT][hapmap]
rs10205083	0.80[YRI][hapmap]
rs11887212	0.91[ASN][1000 genomes]
rs170791	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs186736	0.86[JPT][hapmap]
rs2366157	0.86[JPT][hapmap]
rs333995	0.81[JPT][hapmap]
rs333999	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs334002	0.81[JPT][hapmap]
rs334005	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs334006	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs334007	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs334010	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs334011	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs334014	0.81[JPT][hapmap]
rs334017	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs334035	0.87[JPT][hapmap]
rs334040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs334041	0.93[JPT][hapmap]
rs334042	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs334043	0.87[JPT][hapmap]
rs334044	0.93[JPT][hapmap]
rs334045	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs334102	0.93[JPT][hapmap]
rs334103	0.93[JPT][hapmap]
rs334110	0.93[JPT][hapmap]
rs6433715	0.86[YRI][hapmap]
rs6719178	0.86[JPT][hapmap]
rs7581504	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs9989738	0.81[JPT][hapmap]

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	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised 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	10 gene(s)	inside rSNPs	diseases
4	nsv1011423	chr2:179084407-179166160	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179091200-179115000	Weak transcription	Aorta	Aorta
2	chr2:179101000-179115400	Weak transcription	Gastric	stomach
3	chr2:179104200-179111000	Weak transcription	Left Ventricle	heart
4	chr2:179105400-179120800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:179106200-179109000	Enhancers	Fetal Muscle Leg	muscle
6	chr2:179106400-179108400	Enhancers	Fetal Brain Male	brain
7	chr2:179106600-179115200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr2:179106800-179115200	Weak transcription	Pancreas	Pancrea
9	chr2:179107200-179109000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:179107200-179109200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:179107200-179109600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:179107200-179110200	Weak transcription	HSMMtube	muscle
13	chr2:179107200-179110400	Weak transcription	Right Atrium	heart
14	chr2:179107200-179112400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:179107200-179115400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:179107200-179116000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:179107400-179109400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:179107400-179109600	Weak transcription	K562	blood
19	chr2:179107400-179109800	Weak transcription	HMEC	breast
20	chr2:179107400-179112000	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:179107400-179112000	Weak transcription	HSMM	muscle
22	chr2:179107400-179112400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:179107400-179115200	Weak transcription	Fetal Lung	lung
24	chr2:179107600-179108800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:179107600-179109200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:179107600-179111000	Weak transcription	Brain Angular Gyrus	brain
27	chr2:179107600-179115000	Weak transcription	Fetal Brain Female	brain
28	chr2:179107600-179115400	Weak transcription	Brain Anterior Caudate	brain
29	chr2:179107800-179123000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:179108000-179111600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:179108200-179108400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:179108200-179108800	Weak transcription	Psoas Muscle	Psoas
33	chr2:179108200-179109000	Enhancers	Esophagus	oesophagus
34	chr2:179108200-179112200	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links