Variant report

Variant	rs6545467
Chromosome Location	chr2:55269948-55269949
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55267799..55270095-chr2:55276037..55279766,5	MCF-7	breast:
2	chr2:55257553..55263983-chr2:55266645..55270936,7	K562	blood:
3	chr2:55265645..55268025-chr2:55268205..55270605,2	MCF-7	breast:
4	chr2:55269242..55271326-chr2:55360631..55363213,2	K562	blood:
5	chr2:55255325..55257378-chr2:55267721..55270534,4	MCF-7	breast:
6	chr2:55261058..55265438-chr2:55268460..55270489,4	MCF-7	breast:
7	chr2:55269225..55270745-chr2:55271191..55272770,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10170340	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10189379	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10496036	1.00[JPT][hapmap]
rs12464447	0.89[ASN][1000 genomes]
rs12464595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12475787	0.81[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs12475904	0.92[ASN][1000 genomes]
rs12479297	1.00[ASN][1000 genomes]
rs1348528	0.82[CHB][hapmap]
rs17046570	1.00[JPT][hapmap]
rs17046594	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17347089	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17418675	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1822618	0.82[CHB][hapmap]
rs2864049	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55698303	0.83[ASN][1000 genomes]
rs56013263	0.97[ASN][1000 genomes]
rs6730728	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72795431	0.83[ASN][1000 genomes]
rs72795440	0.87[ASN][1000 genomes]
rs7584354	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584386	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601625	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs887	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
2	chr2:55241000-55272400	Weak transcription	Fetal Kidney	kidney
3	chr2:55250400-55271000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:55250400-55274000	Weak transcription	Pancreas	Pancrea
5	chr2:55253400-55273000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:55254200-55270400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:55255400-55272600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:55255400-55272600	Weak transcription	Fetal Intestine Small	intestine
9	chr2:55256400-55270400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:55259000-55272800	Weak transcription	Small Intestine	intestine
11	chr2:55259200-55272800	Weak transcription	Fetal Heart	heart
12	chr2:55259400-55275200	Weak transcription	Esophagus	oesophagus
13	chr2:55260800-55270400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:55260800-55271200	Weak transcription	Lung	lung
15	chr2:55260800-55271200	Weak transcription	Right Atrium	heart
16	chr2:55260800-55272000	Weak transcription	NH-A	brain
17	chr2:55260800-55272400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:55260800-55273200	Weak transcription	Psoas Muscle	Psoas
19	chr2:55261200-55273000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr2:55261400-55272800	Weak transcription	Thymus	Thymus
21	chr2:55261600-55271200	Weak transcription	Ovary	ovary
22	chr2:55262600-55270200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr2:55264800-55270200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:55264800-55271200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:55265000-55270400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:55265600-55270400	Enhancers	Brain Hippocampus Middle	brain
27	chr2:55266200-55270000	Weak transcription	Hela-S3	cervix
28	chr2:55266200-55271400	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:55266200-55272400	Weak transcription	HMEC	breast
30	chr2:55266200-55272600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:55266200-55273600	Weak transcription	Primary B cells from cord blood	blood
32	chr2:55266400-55270200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr2:55266400-55270200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:55266400-55272000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:55266400-55272600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:55266400-55272600	Weak transcription	Fetal Muscle Leg	muscle
37	chr2:55266800-55270000	Weak transcription	Brain Angular Gyrus	brain
38	chr2:55266800-55272200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:55266800-55273400	Weak transcription	Fetal Thymus	thymus
40	chr2:55267000-55270200	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr2:55267000-55270200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr2:55267000-55270400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:55267000-55270600	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr2:55267000-55270600	Enhancers	Brain Anterior Caudate	brain
45	chr2:55267000-55271000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:55267200-55271400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr2:55267200-55272000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:55267400-55270400	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr2:55267400-55270600	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr2:55267400-55270800	Enhancers	Adipose Nuclei	Adipose

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