Variant report

Variant	rs3755115
Chromosome Location	chr2:53994160-53994161
allele	G/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	HCFC1	chr2:53993642-53995965	Hela-S3	cervix:	n/a	n/a
2	IRF1	chr2:53993929-53995175	K562	blood:	n/a	chr2:53994066-53994078 chr2:53994067-53994077 chr2:53994066-53994078 chr2:53994065-53994079
3	TAL1	chr2:53993741-53995615	K562	blood:	n/a	n/a
4	POLR2A	chr2:53994009-53996575	PBDE	blood:	n/a	n/a
5	POLR2A	chr2:53994089-53995931	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:53994087-53995749	K562	blood:	n/a	n/a
7	TBP	chr2:53993987-53995614	K562	blood:	n/a	n/a
8	POLR2A	chr2:53993983-53998651	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:53994075-53999332	K562	blood:	n/a	n/a
10	JUN	chr2:53994011-53995017	K562	blood:	n/a	chr2:53994827-53994836 chr2:53994843-53994853
11	POLR2A	chr2:53994108-53996420	Hela-S3	cervix:	n/a	n/a
12	MXI1	chr2:53993988-53995837	K562	blood:	n/a	n/a
13	EP300	chr2:53994128-53995703	K562	blood:	n/a	chr2:53994922-53994938
14	POLR2A	chr2:53993996-53995782	GM12891	blood:	n/a	n/a
15	GATA1	chr2:53994002-53995635	PBDE	blood:	n/a	chr2:53994842-53994849

No.	Distal block	Cell Line	Cell type
1	chr2:53780507..53782864-chr2:53992929..53994536,2	K562	blood:
2	chr2:53992980..53996474-chr2:54011575..54015691,9	K562	blood:
3	chr2:53993518..53997677-chr2:54010995..54015634,7	MCF-7	breast:
4	chr2:53993579..53997009-chr2:54011416..54015067,4	MCF-7	breast:

Variant related genes	Relation type
CHAC2	TF binding region
GPR75-ASB3	TF binding region
ENSG00000068912	Chromatin interaction
ENSG00000115239	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10204432	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10490472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10490473	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap]
rs13387421	0.85[EUR][1000 genomes]
rs13404007	0.85[EUR][1000 genomes]
rs13426962	0.87[EUR][1000 genomes]
rs17039534	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17045069	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17045109	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17045123	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17045139	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17045239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17045241	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17045262	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17045286	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17045296	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2056650	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs2287339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2287346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2287347	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs2302876	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2302880	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28834518	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3213768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3213774	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3755113	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs3755114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3755116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3770390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3815650	0.80[EUR][1000 genomes]
rs3821079	0.85[EUR][1000 genomes]
rs59951261	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60972886	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545368	0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs6724214	0.86[ASN][1000 genomes]
rs6761242	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72799242	0.85[EUR][1000 genomes]
rs72799275	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72799277	1.00[AFR][1000 genomes]
rs72799278	1.00[AFR][1000 genomes]
rs72901302	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72902916	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72902923	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72902926	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72902929	0.85[EUR][1000 genomes]
rs7605552	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes]
rs997643	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53937000-53994400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:53937200-53994200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:53937400-53994400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr2:53958200-53994400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:53973400-53994400	Weak transcription	Colonic Mucosa	Colon
6	chr2:53975800-53994400	Weak transcription	Fetal Kidney	kidney
7	chr2:53978800-53994200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:53979800-53994200	Weak transcription	Psoas Muscle	Psoas
9	chr2:53979800-53994200	Weak transcription	NHLF	lung
10	chr2:53982400-53994400	Weak transcription	NHDF-Ad	bronchial
11	chr2:53982800-53994200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:53984200-53994200	Weak transcription	HSMMtube	muscle
13	chr2:53984200-53994400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:53984200-53994400	Weak transcription	Lung	lung
15	chr2:53984200-53994400	Weak transcription	Right Ventricle	heart
16	chr2:53984600-53994400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:53984800-53994200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:53984800-53994400	Weak transcription	Brain Angular Gyrus	brain
19	chr2:53986400-53994600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:53987200-53994400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:53989800-53994200	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:53990800-53994200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:53990800-53994200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:53990800-53994200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr2:53990800-53994200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:53990800-53994200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:53990800-53994200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:53990800-53994200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:53990800-53994200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:53990800-53994200	Weak transcription	Adipose Nuclei	Adipose
31	chr2:53990800-53994200	Weak transcription	Brain Anterior Caudate	brain
32	chr2:53990800-53994200	Weak transcription	Brain Substantia Nigra	brain
33	chr2:53990800-53994200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr2:53990800-53994400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:53990800-53994400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:53990800-53994400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr2:53990800-53994400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:53990800-53994400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr2:53990800-53994400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:53990800-53994400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:53990800-53994400	Weak transcription	Aorta	Aorta
42	chr2:53990800-53994400	Weak transcription	Esophagus	oesophagus
43	chr2:53990800-53994400	Weak transcription	Fetal Brain Male	brain
44	chr2:53990800-53994400	Weak transcription	Placenta	Placenta
45	chr2:53990800-53994400	Weak transcription	Fetal Stomach	stomach
46	chr2:53990800-53994400	Weak transcription	Left Ventricle	heart
47	chr2:53990800-53994400	Weak transcription	Ovary	ovary
48	chr2:53990800-53994400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:53990800-53994600	Weak transcription	Gastric	stomach
50	chr2:53990800-53994600	Weak transcription	Pancreas	Pancrea

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