Variant report

Variant	rs34539547
Chromosome Location	chr2:20236305-20236306
allele	A/G
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	EP300	chr2:20236115-20236309	K562	blood:	n/a	n/a
2	RCOR1	chr2:20236130-20236359	K562	blood:	n/a	n/a
3	POLR2A	chr2:20235999-20236683	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr2:20235713-20237038	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr2:20235963-20236557	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr2:20235651-20236704	K562	blood:	n/a	n/a
7	ELF1	chr2:20236083-20236328	K562	blood:	n/a	chr2:20236217-20236230
8	ELF1	chr2:20236010-20236376	K562	blood:	n/a	chr2:20236217-20236230
9	ATF1	chr2:20236063-20236377	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:20235625..20237177-chr2:20241948..20244789,2	MCF-7	breast:
2	chr2:20235025..20246171-chr2:20248104..20254249,17	MCF-7	breast:
3	chr2:20236235..20238092-chr2:20238674..20240856,2	MCF-7	breast:
4	chr2:20235298..20239645-chr2:20240802..20243443,5	K562	blood:
5	chr2:20236074..20238598-chr2:20248598..20251526,3	K562	blood:

Variant related genes	Relation type
LAPTM4A	TF binding region
ENSG00000223734	Chromatin interaction
ENSG00000068697	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1016316	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11674251	0.87[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11689320	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11689431	0.82[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs11694170	1.00[CEU][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11695154	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1191805	0.86[EUR][1000 genomes]
rs1191817	0.87[EUR][1000 genomes]
rs12988954	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1473887	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1473890	0.94[EUR][1000 genomes]
rs1513830	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1513831	1.00[CEU][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs16987338	0.94[CEU][hapmap];0.92[JPT][hapmap];0.93[EUR][1000 genomes]
rs36071721	0.93[EUR][1000 genomes]
rs3731673	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3769759	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769760	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769762	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62109427	0.86[ASN][1000 genomes]
rs62109431	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706375	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6720508	0.95[EUR][1000 genomes]
rs7558777	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7558988	0.90[EUR][1000 genomes]
rs7570360	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7587612	0.93[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34539547	AC098828.2	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20221400-20249800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:20225400-20240600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:20227000-20239800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:20227000-20240200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:20227000-20240200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:20227000-20240600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:20227000-20240800	Strong transcription	Placenta	Placenta
8	chr2:20227000-20241000	Strong transcription	Liver	Liver
9	chr2:20227000-20242000	Strong transcription	Primary T cells from cord blood	blood
10	chr2:20227000-20242400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr2:20227200-20240200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:20227200-20240800	Strong transcription	Fetal Lung	lung
13	chr2:20227200-20241000	Strong transcription	Fetal Thymus	thymus
14	chr2:20227200-20242200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:20227400-20240800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr2:20227400-20240800	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr2:20227400-20240800	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:20227600-20240400	Strong transcription	Adipose Nuclei	Adipose
19	chr2:20227600-20241000	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:20227800-20241200	Strong transcription	Fetal Intestine Large	intestine
21	chr2:20227800-20242200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:20228000-20237000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:20228000-20240200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:20228000-20240200	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr2:20228000-20240600	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:20228000-20242000	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr2:20228200-20240000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:20228200-20240800	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr2:20228200-20240800	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr2:20228200-20242600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:20228400-20240200	Strong transcription	Osteobl	bone
32	chr2:20228400-20240800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:20228400-20241400	Strong transcription	Dnd41	blood
34	chr2:20228600-20238000	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:20228600-20240400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:20228800-20240800	Strong transcription	Brain Anterior Caudate	brain
37	chr2:20229600-20240800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:20229800-20238200	Strong transcription	Brain Cingulate Gyrus	brain
39	chr2:20229800-20240600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:20229800-20240800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:20229800-20241400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:20230000-20240400	Strong transcription	NHLF	lung
43	chr2:20230000-20242200	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr2:20230200-20240600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:20230200-20240600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:20230200-20241600	Strong transcription	HepG2	liver
47	chr2:20230200-20241800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr2:20230200-20242200	Strong transcription	Fetal Brain Female	brain
49	chr2:20230400-20240200	Strong transcription	HSMM	muscle
50	chr2:20230400-20240400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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