Variant report

Variant	rs2444860
Chromosome Location	chr8:99052895-99052896
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:73)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:73 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:99052838-99053023	ProgFib	skin:	n/a	n/a
2	POLR2A	chr8:99051179-99053626	U87	brain:	n/a	n/a
3	POLR2A	chr8:99052315-99052932	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr8:99052760-99052941	GM12891	blood:	n/a	n/a
5	POLR2A	chr8:99052242-99053979	K562	blood:	n/a	n/a
6	POLR2A	chr8:99051204-99054414	HepG2	liver:	n/a	n/a
7	POLR2A	chr8:99052358-99052986	HUVEC	blood vessel:	n/a	n/a
8	BCL3	chr8:99051723-99053174	A549	lung:	n/a	n/a
9	POLR2A	chr8:99051729-99053403	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr8:99051725-99053690	K562	blood:	n/a	n/a
11	POLR2A	chr8:99052065-99053335	GM12891	blood:	n/a	n/a
12	POLR2A	chr8:99050482-99053738	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr8:99051829-99053306	K562	blood:	n/a	n/a
14	NFATC1	chr8:99052172-99053003	GM12878	blood:	n/a	n/a
15	POLR2A	chr8:99052075-99053032	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr8:99052272-99053074	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr8:99052062-99052911	Raji	blood:	n/a	n/a
18	STAT3	chr8:99052856-99053037	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr8:99051561-99053756	K562	blood:	n/a	n/a
20	POLR2A	chr8:99052876-99053929	K562	blood:	n/a	n/a
21	POLR2A	chr8:99051344-99053825	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr8:99052056-99053885	GM12892	blood:	n/a	n/a
23	POLR2A	chr8:99051108-99053626	U87	brain:	n/a	n/a
24	POLR2A	chr8:99052105-99053916	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr8:99051641-99054099	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr8:99051336-99053836	GM12878	blood:	n/a	n/a
27	POLR2A	chr8:99051912-99053262	GM19099	blood:	n/a	n/a
28	POLR2A	chr8:99052026-99053282	IMR90	lung:	n/a	n/a
29	POLR2A	chr8:99052087-99053310	GM12878	blood:	n/a	n/a
30	POLR2A	chr8:99051852-99053411	K562	blood:	n/a	n/a
31	POLR2A	chr8:99052127-99053686	K562	blood:	n/a	n/a
32	POLR2A	chr8:99051836-99053923	HepG2	liver:	n/a	n/a
33	POLR2A	chr8:99052225-99053547	GM12891	blood:	n/a	n/a
34	PML	chr8:99052293-99053030	K562	blood:	n/a	n/a
35	POLR2A	chr8:99050934-99054545	A549	lung:	n/a	n/a
36	POLR2A	chr8:99052075-99053659	HepG2	liver:	n/a	n/a
37	MTA3	chr8:99052187-99053064	GM12878	blood:	n/a	n/a
38	POLR2A	chr8:99051498-99052955	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr8:99052213-99053288	PBDE	blood:	n/a	n/a
40	POLR2A	chr8:99052041-99053916	GM12892	blood:	n/a	n/a
41	POLR2A	chr8:99052014-99053114	GM12878	blood:	n/a	n/a
42	POLR2A	chr8:99051513-99053621	HCT-116	colon:	n/a	n/a
43	POLR2A	chr8:99052015-99053310	HL-60	blood:	n/a	n/a
44	POLR2A	chr8:99052873-99053581	K562	blood:	n/a	n/a
45	POLR2A	chr8:99050206-99056102	K562	blood:	n/a	n/a
46	BCLAF1	chr8:99052485-99052994	GM12878	blood:	n/a	n/a
47	POLR2A	chr8:99049854-99054372	SK-N-MC	brain:	n/a	n/a
48	POLR2A	chr8:99051220-99053690	GM12878	blood:	n/a	n/a
49	POLR2A	chr8:99051437-99058581	PFSK-1	brain:	n/a	n/a
50	POLR2A	chr8:99050818-99053889	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr8:99051622..99053848-chr8:99067890..99069783,2	K562	blood:
2	chr8:97899859..97901582-chr8:99051432..99053319,2	K562	blood:
3	chr8:99050817..99053848-chr8:99067344..99069783,4	K562	blood:
4	chr8:99011784..99014375-chr8:99051357..99053193,2	MCF-7	breast:
5	chr8:99039776..99042431-chr8:99049506..99054025,4	K562	blood:
6	chr8:99015593..99019656-chr8:99049212..99053715,4	MCF-7	breast:
7	chr8:99039036..99041305-chr8:99052525..99056666,3	K562	blood:
8	chr8:98853571..98856078-chr8:99050894..99053584,2	MCF-7	breast:
9	chr8:99028352..99031100-chr8:99051141..99054386,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000245970	TF binding region
ENSG00000132561	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12545793	0.87[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2248014	0.85[MEX][hapmap]
rs2444891	0.87[ASW][hapmap];0.86[GIH][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2444892	0.85[MEX][hapmap]
rs2513852	0.81[MEX][hapmap]
rs4735522	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62523598	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2444860	LAPTM4B	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99021200-99053600	Weak transcription	A549	lung
2	chr8:99022400-99055200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr8:99024000-99054800	Weak transcription	Right Ventricle	heart
4	chr8:99024200-99055000	Weak transcription	Fetal Brain Male	brain
5	chr8:99024200-99056000	Weak transcription	Spleen	Spleen
6	chr8:99029000-99053600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr8:99030600-99053400	Weak transcription	Pancreas	Pancrea
8	chr8:99030600-99056800	Weak transcription	Aorta	Aorta
9	chr8:99031000-99055400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr8:99033800-99054800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr8:99033800-99055200	Weak transcription	Small Intestine	intestine
12	chr8:99033800-99055600	Weak transcription	Left Ventricle	heart
13	chr8:99034200-99054200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr8:99034200-99054800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr8:99036800-99053200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr8:99037200-99053200	Weak transcription	Fetal Intestine Small	intestine
17	chr8:99037600-99054800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr8:99037600-99056400	Weak transcription	Lung	lung
19	chr8:99039200-99053000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr8:99041400-99053600	Weak transcription	Psoas Muscle	Psoas
21	chr8:99042400-99053000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr8:99043600-99055400	Weak transcription	Esophagus	oesophagus
23	chr8:99044200-99054400	Weak transcription	Brain Germinal Matrix	brain
24	chr8:99044200-99054400	Weak transcription	HepG2	liver
25	chr8:99044600-99054200	Weak transcription	Fetal Lung	lung
26	chr8:99044800-99057000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr8:99045400-99054000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr8:99045400-99054800	Weak transcription	Stomach Mucosa	stomach
29	chr8:99045600-99056800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr8:99045800-99053400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr8:99046000-99053000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr8:99046000-99055200	Weak transcription	Brain Substantia Nigra	brain
33	chr8:99046200-99053200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr8:99046200-99054200	Weak transcription	NHDF-Ad	bronchial
35	chr8:99046200-99054800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr8:99046200-99054800	Weak transcription	Brain Angular Gyrus	brain
37	chr8:99046200-99056400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr8:99046400-99053400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr8:99046400-99054000	Weak transcription	Thymus	Thymus
40	chr8:99046400-99054600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr8:99046400-99055600	Weak transcription	HSMMtube	muscle
42	chr8:99046600-99053800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr8:99046800-99053000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr8:99046800-99054600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr8:99047000-99053800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr8:99047000-99053800	Weak transcription	Primary T cells from cord blood	blood
47	chr8:99047000-99055800	Weak transcription	Ovary	ovary
48	chr8:99047000-99056400	Weak transcription	Colonic Mucosa	Colon
49	chr8:99047200-99054200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr8:99047200-99054800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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