Variant report

Variant	rs4620534
Chromosome Location	chr1:154150448-154150449
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154150440-154150785	GM12878	blood:	n/a	n/a
2	EGR1	chr1:154150441-154150906	K562	blood:	n/a	chr1:154150701-154150710
3	POLR2A	chr1:154150403-154150681	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr1:154150348-154151930	K562	blood:	n/a	n/a
5	POLR2A	chr1:154150303-154151881	PFSK-1	brain:	n/a	n/a
6	GATA1	chr1:154150040-154150915	PBDE	blood:	n/a	chr1:154150682-154150691
7	POLR2A	chr1:154150328-154151967	A549	lung:	n/a	n/a
8	POLR2A	chr1:154150443-154150466	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr1:154149992-154151412	PFSK-1	brain:	n/a	n/a
10	TEAD4	chr1:154150362-154150889	K562	blood:	n/a	n/a
11	POLR2A	chr1:154150022-154152203	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153962189..153967020-chr1:154149779..154153923,7	MCF-7	breast:
2	chr1:154145134..154153289-chr1:154153487..154160631,22	K562	blood:
3	chr1:154142747..154146273-chr1:154146772..154152940,5	K562	blood:
4	chr1:153961855..153964878-chr1:154149314..154153044,5	K562	blood:
5	chr1:154138203..154141121-chr1:154149226..154151416,2	MCF-7	breast:
6	chr1:154149113..154161877-chr1:154185436..154196776,24	K562	blood:
7	chr1:154150174..154152704-chr1:154242243..154245750,3	MCF-7	breast:
8	chr1:154148286..154150697-chr1:154192561..154194921,2	MCF-7	breast:

No data

Variant related genes	Relation type
TPM3	TF binding region
ENSG00000143549	Chromatin interaction
ENSG00000143575	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000264384	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000143612	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10158820	0.91[JPT][hapmap]
rs1044013	0.91[JPT][hapmap]
rs11265238	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11265251	0.91[JPT][hapmap]
rs11265425	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11802893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1194593	0.91[JPT][hapmap]
rs1194594	0.83[YRI][hapmap]
rs1194596	0.91[JPT][hapmap]
rs1194597	0.91[YRI][hapmap]
rs1194601	1.00[YRI][hapmap]
rs1194605	0.81[LWK][hapmap];0.87[YRI][hapmap]
rs12025237	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs12026177	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12026615	0.81[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs12027999	0.84[EUR][1000 genomes]
rs12028949	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12043131	0.90[CEU][hapmap]
rs1205590	0.87[YRI][hapmap]
rs12062977	0.91[JPT][hapmap]
rs12733060	0.84[EUR][1000 genomes]
rs12738393	0.83[EUR][1000 genomes]
rs12745098	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16835846	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16835852	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1760802	0.91[JPT][hapmap]
rs2274993	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs2340473	0.86[JPT][hapmap]
rs2500222	1.00[YRI][hapmap]
rs2633434	0.84[YRI][hapmap]
rs2790689	0.81[CEU][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap]
rs28372838	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2879788	0.91[JPT][hapmap]
rs3002660	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34128679	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34335016	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35761479	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3762340	0.90[CEU][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs3790613	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs3790614	0.84[EUR][1000 genomes]
rs3811453	0.90[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs3811455	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3828077	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs3935419	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4433384	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4459102	0.81[CEU][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap]
rs59651124	0.86[AFR][1000 genomes]
rs60282844	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6427509	0.91[JPT][hapmap]
rs6673752	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs6676022	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6719	0.91[JPT][hapmap]
rs9803857	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
7	nsv1000153	chr1:154074249-154152417	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4620534	SLC27A3	cis	lymphoblastoid	seeQTL
rs4620534	HAX1	cis	cerebellum	SCAN
rs4620534	PIP5K1A	cis	cerebellum	SCAN
rs4620534	UBAP2L	cis	multi-tissue	Pritchard
rs4620534	RAB13	cis	parietal	SCAN
rs4620534	HAX1	cis	parietal	SCAN
rs4620534	C1orf43	cis	parietal	SCAN
rs4620534	HAX1	cis	lymphoblastoid	seeQTL
rs4620534	DENND4B	cis	parietal	SCAN
rs4620534	SCAMP3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154128000-154150800	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr1:154128200-154151200	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:154130200-154150600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:154142400-154152000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:154143800-154153600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
6	chr1:154144200-154154400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:154145600-154150600	Weak transcription	Aorta	Aorta
8	chr1:154145800-154150600	Weak transcription	Ovary	ovary
9	chr1:154145800-154151200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:154145800-154153400	Weak transcription	Fetal Kidney	kidney
11	chr1:154146800-154151000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:154147000-154151400	Genic enhancers	Primary T cells fromperipheralblood	blood
13	chr1:154147200-154152400	Genic enhancers	Primary B cells from peripheral blood	blood
14	chr1:154147800-154152400	Genic enhancers	Primary monocytes fromperipheralblood	blood
15	chr1:154148000-154150600	Genic enhancers	Primary B cells from cord blood	blood
16	chr1:154148000-154150800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr1:154148200-154150800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:154148200-154151000	Enhancers	Colonic Mucosa	Colon
19	chr1:154148200-154153800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:154148400-154151000	Genic enhancers	Fetal Intestine Large	intestine
21	chr1:154148400-154151200	Enhancers	Small Intestine	intestine
22	chr1:154148400-154152400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:154148400-154152800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:154148400-154152800	Genic enhancers	Fetal Thymus	thymus
25	chr1:154148400-154153000	Genic enhancers	Fetal Muscle Leg	muscle
26	chr1:154148600-154150600	Genic enhancers	Hela-S3	cervix
27	chr1:154148600-154150800	Weak transcription	Fetal Lung	lung
28	chr1:154148600-154151200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:154148600-154151200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:154148600-154151200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:154148600-154151400	Enhancers	Liver	Liver
32	chr1:154148600-154151400	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr1:154148600-154152400	Enhancers	Gastric	stomach
34	chr1:154148600-154152600	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr1:154148600-154152600	Enhancers	Stomach Mucosa	stomach
36	chr1:154148600-154152800	Genic enhancers	HMEC	breast
37	chr1:154148600-154154400	Enhancers	Brain Angular Gyrus	brain
38	chr1:154148600-154155000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:154148800-154150600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:154148800-154150600	Weak transcription	Fetal Stomach	stomach
41	chr1:154148800-154150600	Weak transcription	Lung	lung
42	chr1:154148800-154150600	Weak transcription	HSMMtube	muscle
43	chr1:154148800-154150800	Weak transcription	Pancreas	Pancrea
44	chr1:154148800-154151000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:154148800-154151000	Weak transcription	Esophagus	oesophagus
46	chr1:154148800-154151200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:154148800-154151600	Enhancers	Adipose Nuclei	Adipose
48	chr1:154148800-154151800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr1:154148800-154151800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr1:154148800-154152000	Enhancers	Rectal Mucosa Donor 31	rectum

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