Variant report

Variant	rs56180223
Chromosome Location	chr4:129735485-129735486
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:128981555..128983886-chr4:129733528..129735785,3	K562	blood:
2	chr4:129212724..129215636-chr4:129733775..129736025,2	K562	blood:

Variant related genes	Relation type
ENSG00000251432	Chromatin interaction
ENSG00000138709	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs17013730	1.00[ASN][1000 genomes]
rs17013766	1.00[ASN][1000 genomes]
rs17013768	1.00[ASN][1000 genomes]
rs17013775	1.00[ASN][1000 genomes]
rs17013786	1.00[ASN][1000 genomes]
rs17013789	1.00[ASN][1000 genomes]
rs17013807	1.00[ASN][1000 genomes]
rs17013811	1.00[ASN][1000 genomes]
rs17013813	1.00[ASN][1000 genomes]
rs17013815	1.00[ASN][1000 genomes]
rs17013817	1.00[ASN][1000 genomes]
rs17013854	1.00[ASN][1000 genomes]
rs17013862	1.00[ASN][1000 genomes]
rs17013872	1.00[ASN][1000 genomes]
rs17013877	1.00[ASN][1000 genomes]
rs28635430	1.00[ASN][1000 genomes]
rs3816604	1.00[ASN][1000 genomes]
rs55722445	0.89[AMR][1000 genomes]
rs55753141	0.94[AFR][1000 genomes]
rs55764329	0.89[AMR][1000 genomes]
rs57056827	0.82[AFR][1000 genomes]
rs58053026	0.89[AMR][1000 genomes]
rs58296567	1.00[ASN][1000 genomes]
rs58799593	0.82[AFR][1000 genomes]
rs58952520	0.89[AMR][1000 genomes]
rs59682469	1.00[ASN][1000 genomes]
rs60787284	1.00[ASN][1000 genomes]
rs61696721	1.00[ASN][1000 genomes]
rs6813405	1.00[ASN][1000 genomes]
rs6827804	1.00[ASN][1000 genomes]
rs72922049	0.89[AMR][1000 genomes]
rs72922051	0.89[AMR][1000 genomes]
rs73846991	1.00[ASN][1000 genomes]
rs73846992	1.00[AFR][1000 genomes]
rs73846994	0.94[AFR][1000 genomes]
rs73846999	0.94[AFR][1000 genomes]
rs73847310	0.89[AMR][1000 genomes]
rs73850003	1.00[ASN][1000 genomes]
rs73850004	1.00[ASN][1000 genomes]
rs73850005	0.94[AFR][1000 genomes]
rs73850011	0.94[AFR][1000 genomes]
rs73850013	0.94[AFR][1000 genomes]
rs73850016	0.88[AFR][1000 genomes]
rs73850018	0.88[AFR][1000 genomes]
rs73850041	0.82[AFR][1000 genomes]
rs73850062	0.89[AMR][1000 genomes]
rs73850063	0.89[AMR][1000 genomes]
rs7682356	1.00[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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1020801	chr4:129658178-129778086	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv537248	chr4:129658178-129778086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	29 gene(s)	inside rSNPs	diseases
4	nsv822717	chr4:129724785-129739862	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129730400-129735600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:129730400-129736000	Active TSS	H1 Cell Line	embryonic stem cell
3	chr4:129730600-129735600	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr4:129730600-129736600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr4:129734000-129735600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr4:129734000-129736000	Enhancers	Small Intestine	intestine
7	chr4:129734000-129736800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:129734000-129738200	Weak transcription	Pancreas	Pancrea
9	chr4:129734000-129738400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:129734000-129740200	Weak transcription	Gastric	stomach
11	chr4:129734000-129740400	Weak transcription	Lung	lung
12	chr4:129734000-129741600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:129734200-129735600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr4:129734200-129735600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr4:129734200-129735600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:129734200-129738000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr4:129734200-129738800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:129734200-129740000	Weak transcription	Left Ventricle	heart
19	chr4:129734200-129746200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:129734200-129746200	Weak transcription	Ovary	ovary
21	chr4:129734200-129746800	Weak transcription	Fetal Stomach	stomach
22	chr4:129734200-129747000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr4:129734400-129735600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:129734400-129735600	Enhancers	Fetal Heart	heart
25	chr4:129734400-129736600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr4:129734400-129736600	Weak transcription	Thymus	Thymus
27	chr4:129734400-129736600	Weak transcription	HSMM	muscle
28	chr4:129734400-129736800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr4:129734400-129738000	Weak transcription	Right Atrium	heart
30	chr4:129734400-129739600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr4:129734400-129739600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:129734400-129739600	Weak transcription	Psoas Muscle	Psoas
33	chr4:129734400-129739600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr4:129734400-129740000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr4:129734400-129740400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr4:129734400-129740400	Weak transcription	Fetal Intestine Small	intestine
37	chr4:129734400-129740400	Weak transcription	NH-A	brain
38	chr4:129734400-129740800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr4:129734400-129742400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:129734400-129745600	Weak transcription	Fetal Intestine Large	intestine
41	chr4:129734400-129746000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr4:129734400-129746000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr4:129734400-129746200	Weak transcription	Fetal Muscle Leg	muscle
44	chr4:129734400-129751600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr4:129734400-129756400	Weak transcription	Aorta	Aorta
46	chr4:129734600-129735600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:129734600-129735600	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr4:129734600-129735600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr4:129734600-129735600	Enhancers	HepG2	liver
50	chr4:129734600-129736600	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links