Variant report

Variant	rs28624232
Chromosome Location	chr4:129740399-129740400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:129732203..129736510-chr4:129738670..129742463,5	MCF-7	breast:
2	chr4:129739255..129743318-chr4:129756229..129760124,4	K562	blood:
3	chr4:129730289..129733712-chr4:129739240..129742412,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077684	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10006958	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28430630	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28434631	1.00[AMR][1000 genomes]
rs28583676	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28707598	0.81[AFR][1000 genomes];1.00[AMR][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	nsv517249	chr4:129738328-129927804	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129734000-129740400	Weak transcription	Lung	lung
2	chr4:129734000-129741600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:129734200-129746200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr4:129734200-129746200	Weak transcription	Ovary	ovary
5	chr4:129734200-129746800	Weak transcription	Fetal Stomach	stomach
6	chr4:129734200-129747000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:129734400-129740400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr4:129734400-129740400	Weak transcription	Fetal Intestine Small	intestine
9	chr4:129734400-129740400	Weak transcription	NH-A	brain
10	chr4:129734400-129740800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:129734400-129742400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:129734400-129745600	Weak transcription	Fetal Intestine Large	intestine
13	chr4:129734400-129746000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:129734400-129746000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:129734400-129746200	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:129734400-129751600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr4:129734400-129756400	Weak transcription	Aorta	Aorta
18	chr4:129734600-129740400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:129734600-129740800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr4:129734600-129743200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:129734600-129743800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:129734600-129743800	Weak transcription	NHEK	skin
23	chr4:129734600-129745600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:129734600-129746400	Weak transcription	Right Ventricle	heart
25	chr4:129735000-129740400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:129735000-129743200	Weak transcription	Adipose Nuclei	Adipose
27	chr4:129735000-129747000	Weak transcription	Primary B cells from cord blood	blood
28	chr4:129735200-129746400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr4:129735400-129740600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr4:129735400-129744000	Weak transcription	Hela-S3	cervix
31	chr4:129735400-129748200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:129735400-129752200	Weak transcription	Fetal Brain Female	brain
33	chr4:129736400-129741800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
34	chr4:129736600-129740400	Genic enhancers	HUES64 Cell Line	embryonic stem cell
35	chr4:129736600-129741200	Genic enhancers	A549	lung
36	chr4:129736600-129741800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
37	chr4:129736600-129744600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr4:129737000-129740800	Enhancers	Osteobl	bone
39	chr4:129737000-129741000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:129737000-129743200	Weak transcription	HUVEC	blood vessel
41	chr4:129737400-129740600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr4:129737400-129741200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
43	chr4:129737600-129741200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr4:129737600-129741800	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr4:129737800-129741200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr4:129737800-129744800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr4:129738400-129740600	Enhancers	NHDF-Ad	bronchial
48	chr4:129738400-129744400	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr4:129738600-129740400	Weak transcription	HSMM	muscle
50	chr4:129738600-129740600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links