Variant report

Variant	rs12508128
Chromosome Location	chr4:104011241-104011242
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103998136..104000908-chr4:104009280..104011313,3	K562	blood:
2	chr4:104009215..104010720-chr4:104010992..104013903,2	K562	blood:
3	chr4:104007330..104009094-chr4:104010936..104013359,2	K562	blood:

Variant related genes	Relation type
ENSG00000164038	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10516497	0.93[CEU][hapmap]
rs11729250	0.80[ASN][1000 genomes]
rs11734396	0.87[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12505012	0.81[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12506575	0.81[CEU][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17033423	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17217250	0.81[CEU][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs17283278	0.87[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs2243682	0.87[CEU][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2290943	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs2615538	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2615541	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2615542	0.87[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2623062	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2623063	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2623069	0.87[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2623076	0.81[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2623082	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2711888	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2711889	0.87[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2711891	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2711893	0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2711895	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2711896	0.87[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2711900	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2711901	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2720447	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2720449	0.87[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2720450	0.87[AMR][1000 genomes]
rs2720451	0.81[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2720452	0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2720453	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2720455	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2720456	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2720457	0.81[CEU][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2720463	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2720465	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2720467	0.81[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2720470	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3816642	0.84[EUR][1000 genomes]
rs4698879	0.87[CEU][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs55708783	0.87[EUR][1000 genomes]
rs55777543	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58477215	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68023422	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6830082	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs6847142	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs6847357	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs72665085	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72665089	0.87[EUR][1000 genomes]
rs7672974	0.81[CEU][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9994654	0.93[CEU][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	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers 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	36 gene(s)	inside rSNPs	diseases
2	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers 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	36 gene(s)	inside rSNPs	diseases
3	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv830021	chr4:103934454-104100588	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	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	chr4:103998200-104020400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:103998400-104018800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:103998600-104011600	Weak transcription	NHDF-Ad	bronchial
4	chr4:103998600-104020200	Weak transcription	Fetal Brain Male	brain
5	chr4:103998800-104013400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:103998800-104019600	Weak transcription	NHEK	skin
7	chr4:103999000-104020200	Weak transcription	Hela-S3	cervix
8	chr4:103999400-104013600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr4:104000000-104012400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:104000200-104016400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:104000400-104012400	Strong transcription	Duodenum Mucosa	Duodenum
12	chr4:104000400-104014600	Strong transcription	Fetal Intestine Large	intestine
13	chr4:104000600-104016400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:104000800-104012800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:104000800-104013000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:104000800-104013600	Strong transcription	Primary T cells from cord blood	blood
17	chr4:104001000-104012400	Strong transcription	Liver	Liver
18	chr4:104001600-104013800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:104001800-104012400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:104001800-104015000	Strong transcription	Fetal Lung	lung
21	chr4:104002000-104012800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:104003200-104013200	Strong transcription	HSMM	muscle
23	chr4:104005000-104013600	Strong transcription	Fetal Muscle Trunk	muscle
24	chr4:104005000-104014000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:104005200-104013000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:104005200-104013400	Strong transcription	Adipose Nuclei	Adipose
27	chr4:104005400-104012200	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr4:104005400-104012400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:104005400-104012400	Strong transcription	Stomach Smooth Muscle	stomach
30	chr4:104005400-104012600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:104005400-104012600	Strong transcription	Ovary	ovary
32	chr4:104005400-104012600	Strong transcription	Dnd41	blood
33	chr4:104005400-104014800	Strong transcription	Fetal Muscle Leg	muscle
34	chr4:104005400-104015600	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr4:104005400-104016400	Strong transcription	Fetal Thymus	thymus
36	chr4:104005600-104012400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:104005600-104012400	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr4:104006000-104012400	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:104006000-104012600	Strong transcription	Primary hematopoietic stem cells	blood
40	chr4:104006200-104012400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr4:104006200-104012400	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr4:104006200-104012400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr4:104006400-104012200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:104006400-104012400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:104006400-104012400	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr4:104006400-104012400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr4:104006400-104012400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr4:104006400-104012400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr4:104006400-104012400	Strong transcription	Brain Substantia Nigra	brain
50	chr4:104006400-104012600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links