Variant report

Variant	rs17347089
Chromosome Location	chr2:55257409-55257410
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55255815..55260220-chr2:55273453..55278520,8	MCF-7	breast:
2	chr2:55256333..55257873-chr2:55260544..55262457,2	MCF-7	breast:
3	chr2:55255186..55258524-chr2:55346221..55348339,3	K562	blood:
4	chr2:55252582..55260799-chr2:55274165..55279100,17	MCF-7	breast:
5	chr2:55256373..55258022-chr2:55400238..55403014,2	K562	blood:
6	chr2:55255745..55260236-chr2:55263069..55266549,5	K562	blood:
7	chr2:55257154..55258943-chr2:55260166..55262885,2	K562	blood:
8	chr2:55256384..55258349-chr2:55263077..55265384,2	K562	blood:
9	chr2:55246557..55249520-chr2:55255135..55258063,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10189379	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10496036	0.92[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs12464447	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12464595	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12475787	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12475904	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12479297	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17046570	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17046594	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17418675	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2289747	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55659423	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55698303	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55993793	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56013263	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545467	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6707036	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs67156582	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6730728	0.95[ASN][1000 genomes]
rs72795431	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72795440	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7582359	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs7584354	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7584386	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7601625	1.00[JPT][hapmap];0.86[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:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
2	chr2:55237600-55258600	Weak transcription	Ovary	ovary
3	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
4	chr2:55241000-55272400	Weak transcription	Fetal Kidney	kidney
5	chr2:55242400-55258000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:55243000-55262400	Weak transcription	Hela-S3	cervix
7	chr2:55243800-55259800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:55245600-55265600	Weak transcription	Stomach Mucosa	stomach
9	chr2:55246800-55259800	Weak transcription	NH-A	brain
10	chr2:55248200-55258400	Weak transcription	Lung	lung
11	chr2:55248200-55259200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:55250000-55260000	Weak transcription	Gastric	stomach
13	chr2:55250400-55271000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:55250400-55274000	Weak transcription	Pancreas	Pancrea
15	chr2:55250600-55258400	Weak transcription	Spleen	Spleen
16	chr2:55251400-55258000	Weak transcription	Fetal Heart	heart
17	chr2:55251400-55259400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr2:55252400-55259000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr2:55252600-55258400	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:55252600-55261400	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr2:55253400-55273000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr2:55253600-55257600	Weak transcription	Fetal Brain Female	brain
23	chr2:55253600-55258400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:55253800-55260400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:55253800-55260600	Weak transcription	Right Atrium	heart
26	chr2:55253800-55261400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr2:55254200-55269800	Weak transcription	Aorta	Aorta
28	chr2:55254200-55270400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:55254400-55262600	Enhancers	Brain Hippocampus Middle	brain
30	chr2:55254600-55258400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr2:55254600-55258400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr2:55254600-55258400	Weak transcription	Psoas Muscle	Psoas
33	chr2:55254600-55258800	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr2:55254600-55259800	Weak transcription	Primary B cells from cord blood	blood
35	chr2:55254600-55259800	Weak transcription	Thymus	Thymus
36	chr2:55254600-55260000	Weak transcription	Fetal Thymus	thymus
37	chr2:55254600-55260600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:55254800-55258000	Weak transcription	HMEC	breast
39	chr2:55254800-55260000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr2:55254800-55260400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:55254800-55265000	Enhancers	Brain Substantia Nigra	brain
42	chr2:55255000-55259400	Enhancers	Muscle Satellite Cultured Cells	--
43	chr2:55255000-55260600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr2:55255200-55257600	Weak transcription	Fetal Brain Male	brain
45	chr2:55255200-55258200	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr2:55255200-55261200	Weak transcription	HUVEC	blood vessel
47	chr2:55255400-55257800	Weak transcription	Osteobl	bone
48	chr2:55255400-55258000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr2:55255400-55258600	Weak transcription	Small Intestine	intestine
50	chr2:55255400-55259800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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