Variant report

Variant	rs17139898
Chromosome Location	chr5:115817842-115817843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:115817743-115818319	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr5:115817753-115818393	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr5:115817777-115818331	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr5:115814059-115818431	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:115796425..115798822-chr5:115817832..115819874,2	K562	blood:
2	chr5:115816747..115819335-chr5:115820199..115822889,2	MCF-7	breast:
3	chr5:115815911..115818115-chr5:115838148..115840326,2	K562	blood:

Variant related genes	Relation type
SEMA6A	TF binding region
ENSG00000092421	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10077506	0.89[CEU][hapmap]
rs10077720	0.89[CEU][hapmap]
rs10078884	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11956022	0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12186896	0.94[JPT][hapmap]
rs12522475	0.82[EUR][1000 genomes]
rs154599	0.84[JPT][hapmap]
rs154600	0.89[JPT][hapmap]
rs17139825	0.89[CEU][hapmap]
rs17139903	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[ASN][1000 genomes]
rs17139927	0.88[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2059874	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2161227	0.88[CEU][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs2278263	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278265	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2287685	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9885339	0.84[JPT][hapmap]
rs9885340	0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115783600-115829600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:115791600-115838000	Weak transcription	Right Ventricle	heart
3	chr5:115796000-115833400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:115797000-115834800	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr5:115797000-115838400	Strong transcription	Placenta	Placenta
6	chr5:115797400-115833800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:115797600-115834600	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr5:115797800-115834800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:115798000-115833200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:115798000-115834600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:115799000-115830400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:115799400-115832000	Strong transcription	Fetal Muscle Trunk	muscle
13	chr5:115801400-115824000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:115801400-115825000	Weak transcription	Psoas Muscle	Psoas
15	chr5:115803400-115833200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
16	chr5:115804600-115822600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:115808800-115818200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr5:115810800-115821200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:115811800-115818200	Strong transcription	Fetal Brain Female	brain
20	chr5:115812200-115818400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr5:115812600-115818600	Strong transcription	Colonic Mucosa	Colon
22	chr5:115813200-115818400	Strong transcription	Brain Germinal Matrix	brain
23	chr5:115813200-115819200	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:115813200-115824400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:115813200-115826200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr5:115813400-115818400	Strong transcription	Fetal Kidney	kidney
27	chr5:115813400-115820800	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr5:115813400-115822400	Strong transcription	Fetal Intestine Large	intestine
29	chr5:115813600-115818000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr5:115813600-115821400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr5:115813600-115826800	Strong transcription	Fetal Muscle Leg	muscle
32	chr5:115813600-115831800	Strong transcription	Fetal Stomach	stomach
33	chr5:115813600-115832000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr5:115813800-115818200	Strong transcription	Stomach Smooth Muscle	stomach
35	chr5:115813800-115818400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr5:115813800-115818400	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr5:115813800-115818800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:115813800-115822600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:115813800-115827200	Weak transcription	Primary T cells from cord blood	blood
40	chr5:115813800-115830600	Weak transcription	HepG2	liver
41	chr5:115813800-115833600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:115813800-115851000	Weak transcription	Liver	Liver
43	chr5:115814000-115821200	Weak transcription	Adipose Nuclei	Adipose
44	chr5:115814000-115826800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr5:115814000-115830200	Weak transcription	Esophagus	oesophagus
46	chr5:115814000-115850200	Weak transcription	Small Intestine	intestine
47	chr5:115814200-115818200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr5:115814800-115823800	Weak transcription	Colon Smooth Muscle	Colon
49	chr5:115814800-115827800	Weak transcription	Fetal Heart	heart
50	chr5:115815000-115819000	Strong transcription	Fetal Lung	lung

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