Variant report

Variant	rs6005874
Chromosome Location	chr22:29173898-29173899
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29165808..29174203-chr22:29186827..29200037,34	MCF-7	breast:
2	chr22:29172058..29177577-chr22:29178390..29181662,9	MCF-7	breast:
3	chr22:29165791..29171536-chr22:29171828..29178249,15	MCF-7	breast:
4	chr22:29167384..29172904-chr22:29173066..29177227,7	K562	blood:

Variant related genes	Relation type
ENSG00000226471	Chromatin interaction
ENSG00000100219	Chromatin interaction
ENSG00000159873	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10427858	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12330071	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2206061	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2228260	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41281603	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56119508	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5997401	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005861	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6005870	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005898	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005899	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005923	0.86[EUR][1000 genomes]
rs6005924	0.86[EUR][1000 genomes]
rs6005926	0.86[EUR][1000 genomes]
rs9306460	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9625551	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9625565	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9625575	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9625580	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29169800-29179600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:29169800-29180000	Weak transcription	Colonic Mucosa	Colon
3	chr22:29169800-29180200	Weak transcription	Stomach Mucosa	stomach
4	chr22:29169800-29190400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr22:29170000-29174800	Weak transcription	K562	blood
6	chr22:29170000-29176400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr22:29170000-29176400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr22:29170000-29177600	Weak transcription	Aorta	Aorta
9	chr22:29170000-29179200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr22:29170000-29179600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr22:29170000-29182200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr22:29170000-29190200	Weak transcription	Fetal Heart	heart
13	chr22:29170000-29194200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr22:29170200-29175600	Weak transcription	NHDF-Ad	bronchial
15	chr22:29170200-29177800	Weak transcription	HMEC	breast
16	chr22:29170200-29178000	Weak transcription	Brain Anterior Caudate	brain
17	chr22:29170200-29178800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr22:29170200-29182400	Strong transcription	Fetal Stomach	stomach
19	chr22:29170400-29174000	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr22:29170400-29174400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr22:29170400-29175400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr22:29170400-29175600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr22:29170400-29177800	Strong transcription	Fetal Intestine Large	intestine
24	chr22:29170400-29183800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr22:29170400-29184000	Strong transcription	Fetal Muscle Leg	muscle
26	chr22:29170400-29185600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr22:29170600-29174400	Strong transcription	Osteobl	bone
28	chr22:29170600-29174600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr22:29170600-29184600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr22:29170600-29184800	Strong transcription	Fetal Muscle Trunk	muscle
31	chr22:29170600-29185400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr22:29170600-29186000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr22:29170600-29186400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr22:29170800-29174200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr22:29170800-29174200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr22:29170800-29174400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr22:29170800-29174600	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr22:29170800-29174600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
39	chr22:29170800-29175000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr22:29170800-29175000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr22:29170800-29175000	Weak transcription	Psoas Muscle	Psoas
42	chr22:29170800-29179800	Weak transcription	Fetal Brain Male	brain
43	chr22:29170800-29186400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr22:29171000-29174800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr22:29171000-29175400	Weak transcription	Colon Smooth Muscle	Colon
46	chr22:29171000-29175600	Strong transcription	Fetal Intestine Small	intestine
47	chr22:29171000-29175800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr22:29171000-29176400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr22:29171000-29176400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr22:29171000-29178000	Weak transcription	Brain Angular Gyrus	brain

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