Variant report

Variant	rs9646744
Chromosome Location	chr2:153577013-153577014
allele	A/G
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:1)
LncRNA
region (count:1)
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	chr2:153576296-153577186	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr2:153573287-153577046	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:153576605-153577151	MCF-7	breast:	n/a	n/a
4	POLR2A	chr2:153572488-153577031	K562	blood:	n/a	n/a
5	POLR2A	chr2:153576295-153577183	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:153573281-153577192	K562	blood:	n/a	n/a
7	POLR2A	chr2:153572690-153577175	GM12891	blood:	n/a	n/a
8	POLR2A	chr2:153576724-153577103	K562	blood:	n/a	n/a
9	POLR2A	chr2:153573393-153577014	K562	blood:	n/a	n/a
10	POLR2A	chr2:153573356-153577814	K562	blood:	n/a	n/a
11	POLR2A	chr2:153573252-153577227	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:153574994..153576922-chr2:153576951..153581012,5	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARL6IP6-2	chr2:153576681-153577100	NONHSAT074992

No data

Variant related genes	Relation type
PRPF40A	TF binding region
ENSG00000177917	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10172024	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181485	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10200667	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036526	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1065266	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10931229	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1128804	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11544718	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11899051	0.87[ASN][1000 genomes]
rs12477881	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12621561	0.88[ASN][1000 genomes]
rs12997814	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13005368	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13010731	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13017428	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13031469	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13419068	0.88[ASN][1000 genomes]
rs1370498	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1437678	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16831548	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16831740	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17328734	1.00[ASN][1000 genomes]
rs17400645	0.90[ASN][1000 genomes]
rs1962313	0.90[ASN][1000 genomes]
rs1986743	0.87[ASN][1000 genomes]
rs1992146	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2118377	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304559	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2346534	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2346539	0.88[ASN][1000 genomes]
rs2346540	0.88[ASN][1000 genomes]
rs2346541	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346542	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346543	0.90[ASN][1000 genomes]
rs2346549	0.90[ASN][1000 genomes]
rs2346550	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3171980	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34585982	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34668102	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3748937	0.90[ASN][1000 genomes]
rs3748938	0.87[ASN][1000 genomes]
rs3748939	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762503	0.88[ASN][1000 genomes]
rs3762506	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3762507	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3811566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233660	0.90[ASN][1000 genomes]
rs4267470	0.90[ASN][1000 genomes]
rs4580346	0.84[ASN][1000 genomes]
rs4664121	0.88[ASN][1000 genomes]
rs4664122	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4664601	0.88[ASN][1000 genomes]
rs4664602	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4664604	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4664605	0.90[ASN][1000 genomes]
rs4664606	0.89[ASN][1000 genomes]
rs4664607	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4664609	0.90[ASN][1000 genomes]
rs4664610	0.88[ASN][1000 genomes]
rs55785027	0.84[EUR][1000 genomes]
rs56283545	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61049574	0.82[ASN][1000 genomes]
rs6434161	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434162	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713779	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6723574	0.86[ASN][1000 genomes]
rs6727279	0.87[ASN][1000 genomes]
rs6746079	0.88[ASN][1000 genomes]
rs6746321	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6748160	0.90[ASN][1000 genomes]
rs715047	0.86[ASN][1000 genomes]
rs72871191	0.88[ASN][1000 genomes]
rs72872607	0.88[ASN][1000 genomes]
rs7556673	0.88[ASN][1000 genomes]
rs7558920	0.88[ASN][1000 genomes]
rs7559219	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560393	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570759	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7576152	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7576847	0.81[ASN][1000 genomes]
rs7582253	0.88[ASN][1000 genomes]
rs7589899	0.82[ASN][1000 genomes]
rs7592669	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593347	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7599946	0.90[ASN][1000 genomes]
rs7605709	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608603	0.90[ASN][1000 genomes]
rs9288121	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9288125	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9288127	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9789505	0.88[ASN][1000 genomes]
rs9789521	0.87[ASN][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	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3693438	chr2:153505376-153718246	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153575800-153577400	Flanking Active TSS	Fetal Brain Female	brain
2	chr2:153575800-153582800	Weak transcription	Lung	lung
3	chr2:153575800-153587200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:153575800-153611600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:153575800-153611600	Weak transcription	Esophagus	oesophagus
6	chr2:153575800-153621400	Weak transcription	Pancreas	Pancrea
7	chr2:153576000-153577200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:153576000-153577200	Enhancers	Primary B cells from peripheral blood	blood
9	chr2:153576000-153577200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:153576000-153577200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr2:153576000-153577400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:153576000-153577400	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr2:153576000-153577600	Enhancers	Primary T cells fromperipheralblood	blood
14	chr2:153576000-153577800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:153576000-153578000	Weak transcription	Small Intestine	intestine
16	chr2:153576000-153578400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr2:153576000-153579200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:153576000-153581200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:153576000-153594400	Weak transcription	Left Ventricle	heart
20	chr2:153576000-153615800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:153576200-153577200	Enhancers	Primary hematopoietic stem cells	blood
22	chr2:153576200-153577200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr2:153576200-153577200	Enhancers	Brain Hippocampus Middle	brain
24	chr2:153576200-153577200	Enhancers	Brain Substantia Nigra	brain
25	chr2:153576200-153577200	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr2:153576200-153577400	Enhancers	Liver	Liver
27	chr2:153576200-153577400	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr2:153576200-153577400	Enhancers	Thymus	Thymus
29	chr2:153576200-153577600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr2:153576200-153577600	Enhancers	Fetal Intestine Small	intestine
31	chr2:153576200-153578000	Enhancers	Stomach Mucosa	stomach
32	chr2:153576200-153578200	Weak transcription	HSMM	muscle
33	chr2:153576200-153578400	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr2:153576200-153578400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr2:153576200-153578600	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr2:153576200-153594800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr2:153576400-153577200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:153576400-153577200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:153576400-153577200	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr2:153576400-153577200	Flanking Active TSS	Fetal Brain Male	brain
41	chr2:153576400-153577200	Flanking Active TSS	Fetal Heart	heart
42	chr2:153576400-153577200	Enhancers	Spleen	Spleen
43	chr2:153576400-153577200	Flanking Active TSS	NHDF-Ad	bronchial
44	chr2:153576600-153577200	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:153576600-153577200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr2:153576600-153577200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:153576600-153577200	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:153576600-153577200	Enhancers	Primary T cells from cord blood	blood
49	chr2:153576600-153577200	Flanking Active TSS	Brain Germinal Matrix	brain
50	chr2:153576600-153577200	Transcr. at gene 5' and 3'	Fetal Lung	lung

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