Variant report

Variant	rs3853188
Chromosome Location	chr4:77109580-77109581
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:77068157..77072103-chr4:77105294..77112080,6	K562	blood:
2	chr4:77099739..77102113-chr4:77107352..77109592,2	K562	blood:
3	chr4:77101177..77103136-chr4:77108889..77111010,2	MCF-7	breast:
4	chr4:77108730..77110793-chr4:77112512..77115192,2	K562	blood:

Variant related genes	Relation type
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12641190	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13111705	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13117802	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13119254	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1441923	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1470191	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1470192	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1470193	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1470194	0.96[EUR][1000 genomes]
rs1550556	0.95[EUR][1000 genomes]
rs17001588	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17001589	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17001604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2034002	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2034003	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2053486	0.95[EUR][1000 genomes]
rs2053487	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2304813	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304814	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2869854	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34022163	0.96[EUR][1000 genomes]
rs34334700	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34974381	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35583533	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35783378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36035650	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36081173	0.96[EUR][1000 genomes]
rs3796497	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3853189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3853190	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3866353	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3866354	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4452450	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4634246	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4859428	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4859623	0.95[EUR][1000 genomes]
rs4859624	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4859625	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859627	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859628	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859629	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859631	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67653006	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67917805	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6824367	0.96[EUR][1000 genomes]
rs6831345	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6851995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72857046	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72857048	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7664889	0.91[EUR][1000 genomes]
rs7691447	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs894244	0.96[EUR][1000 genomes]
rs894247	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs894248	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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	nsv461558	chr4:77033725-77115553	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv594694	chr4:77033725-77115553	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1000178	chr4:77053046-77113080	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77070600-77113600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr4:77071200-77113600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:77080600-77113600	Weak transcription	Thymus	Thymus
4	chr4:77083200-77112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:77090000-77113600	Weak transcription	A549	lung
6	chr4:77090200-77113000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:77090200-77114800	Weak transcription	Hela-S3	cervix
8	chr4:77091000-77114200	Weak transcription	HMEC	breast
9	chr4:77094400-77113800	Weak transcription	Fetal Thymus	thymus
10	chr4:77095000-77113400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:77096200-77113200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr4:77096200-77113400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:77096800-77114000	Weak transcription	Small Intestine	intestine
14	chr4:77097000-77113200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:77097000-77113200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:77097000-77113200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr4:77097200-77112400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr4:77097200-77113600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:77097400-77113400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr4:77097400-77113400	Weak transcription	Fetal Brain Male	brain
21	chr4:77097400-77115000	Weak transcription	NH-A	brain
22	chr4:77097600-77119600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:77097800-77113400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr4:77098000-77113000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr4:77100000-77112600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:77100400-77113000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:77100800-77112200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr4:77101000-77110200	Weak transcription	Primary T cells from cord blood	blood
29	chr4:77101000-77113400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr4:77101400-77112200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr4:77101400-77112400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:77101400-77113000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr4:77101400-77113000	Weak transcription	Dnd41	blood
34	chr4:77101400-77113400	Weak transcription	HSMMtube	muscle
35	chr4:77101400-77114200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:77101600-77112400	Weak transcription	Brain Germinal Matrix	brain
37	chr4:77104000-77112400	Weak transcription	NHEK	skin
38	chr4:77104600-77113800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr4:77105600-77115000	Weak transcription	Fetal Heart	heart
40	chr4:77107200-77110400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:77107200-77113200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:77107200-77113200	Weak transcription	Fetal Kidney	kidney
43	chr4:77107400-77109600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr4:77107400-77110800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:77107400-77112400	Enhancers	Brain Substantia Nigra	brain
46	chr4:77107400-77113000	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr4:77107600-77109600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr4:77107600-77109800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:77107600-77110000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr4:77107600-77111000	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links