Variant report

Variant	rs317854
Chromosome Location	chr4:16163265-16163266
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:16152453..16154569-chr4:16162351..16164254,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10006159	0.82[YRI][hapmap]
rs10019399	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1025897	0.80[YRI][hapmap]
rs1046234	0.85[YRI][hapmap]
rs10516299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10939651	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10939652	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12506249	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12646600	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13133263	0.95[YRI][hapmap]
rs13634	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs1373112	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1619904	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1662650	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1662654	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1662656	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16893162	0.95[YRI][hapmap]
rs1712492	0.95[YRI][hapmap]
rs178450	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs203434	0.90[YRI][hapmap]
rs2044195	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28453363	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28618674	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28645901	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs317853	0.82[AFR][1000 genomes]
rs317855	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs317869	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs317870	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs317871	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs317872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs317873	0.95[YRI][hapmap]
rs317874	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs317875	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs317876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs317877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs317878	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4395495	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6812660	0.95[YRI][hapmap]
rs7657191	0.80[ASN][1000 genomes]
rs894639	0.80[CEU][hapmap]
rs961449	0.90[YRI][hapmap]

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	nsv998299	chr4:16031459-16226466	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16150800-16166600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:16152000-16163800	Weak transcription	Thymus	Thymus
3	chr4:16153000-16163600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:16153000-16164400	Weak transcription	NH-A	brain
5	chr4:16153200-16165200	Weak transcription	HSMM	muscle
6	chr4:16153600-16165600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:16154800-16164400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr4:16157000-16164400	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:16157200-16166800	Weak transcription	Brain Angular Gyrus	brain
10	chr4:16157400-16164200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr4:16157600-16163600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr4:16157600-16164600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:16157800-16164400	Weak transcription	Brain Anterior Caudate	brain
14	chr4:16157800-16164600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:16157800-16170600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr4:16157800-16180000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr4:16157800-16180400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:16158000-16165000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr4:16158000-16175400	Weak transcription	NHDF-Ad	bronchial
20	chr4:16158200-16163600	Weak transcription	Spleen	Spleen
21	chr4:16158200-16163800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:16158200-16164400	Weak transcription	Fetal Stomach	stomach
23	chr4:16158400-16163800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr4:16159000-16163800	Enhancers	Fetal Intestine Large	intestine
25	chr4:16159400-16164600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr4:16159600-16163400	Weak transcription	Dnd41	blood
27	chr4:16159600-16164000	Enhancers	Stomach Mucosa	stomach
28	chr4:16159600-16164800	Weak transcription	K562	blood
29	chr4:16159800-16163800	Weak transcription	Brain Substantia Nigra	brain
30	chr4:16159800-16167400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:16160000-16164600	Weak transcription	Brain Germinal Matrix	brain
32	chr4:16160000-16167600	Weak transcription	HepG2	liver
33	chr4:16160200-16163600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:16160200-16163600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:16160200-16163600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr4:16160200-16163800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:16160200-16163800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:16160200-16164000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:16160200-16164000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:16160200-16164400	Weak transcription	Fetal Brain Female	brain
41	chr4:16160200-16164600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:16160200-16164600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:16160200-16164800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr4:16160200-16165000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr4:16160200-16173800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr4:16160400-16163800	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr4:16160400-16163800	Weak transcription	Right Atrium	heart
48	chr4:16160400-16164600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr4:16160400-16164600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr4:16160400-16164800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links