Variant report

Variant	rs17581939
Chromosome Location	chr2:33497099-33497100
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	RUNX3	chr2:33496967-33497618	GM12878	blood:	n/a	n/a
2	BCL11A	chr2:33497083-33497403	GM12878	blood:	n/a	n/a
3	MEF2A	chr2:33496966-33497552	GM12878	blood:	n/a	n/a
4	FOXM1	chr2:33497007-33497529	GM12878	blood:	n/a	n/a
5	TBL1XR1	chr2:33497093-33497476	GM12878	blood:	n/a	n/a
6	IRF4	chr2:33497026-33497430	GM12878	blood:	n/a	chr2:33497234-33497248
7	BATF	chr2:33497045-33497444	GM12878	blood:	n/a	n/a
8	EP300	chr2:33497082-33497496	GM12878	blood:	n/a	n/a
9	RUNX3	chr2:33496963-33497591	GM12878	blood:	n/a	n/a
10	BATF	chr2:33497054-33497437	GM12878	blood:	n/a	n/a
11	PAX5	chr2:33497048-33497386	GM12892	blood:	n/a	n/a
12	PAX5	chr2:33497068-33497451	GM12878	blood:	n/a	n/a
13	STAT5A	chr2:33497028-33497540	GM12878	blood:	n/a	n/a
14	NFIC	chr2:33497009-33497557	GM12878	blood:	n/a	n/a
15	BCLAF1	chr2:33497006-33497541	GM12878	blood:	n/a	n/a
16	MTA3	chr2:33496936-33497599	GM12878	blood:	n/a	n/a
17	PAX5	chr2:33497036-33497419	GM12878	blood:	n/a	n/a
18	PAX5	chr2:33497083-33497447	GM12891	blood:	n/a	n/a
19	ATF2	chr2:33497053-33497565	GM12878	blood:	n/a	n/a
20	POU2F2	chr2:33497023-33497520	GM12878	blood:	n/a	chr2:33497047-33497058 chr2:33497214-33497227 chr2:33497047-33497058 chr2:33497209-33497230 chr2:33497047-33497057
21	BCL11A	chr2:33497029-33497472	GM12878	blood:	n/a	n/a
22	PAX5	chr2:33496999-33497518	GM12878	blood:	n/a	n/a
23	IRF4	chr2:33497025-33497488	GM12878	blood:	n/a	chr2:33497234-33497248
24	NFATC1	chr2:33497015-33497526	GM12878	blood:	n/a	n/a
25	TCF3	chr2:33496987-33497523	GM12878	blood:	n/a	n/a
26	EP300	chr2:33497098-33497435	GM12878	blood:	n/a	n/a
27	RCOR1	chr2:33497093-33497485	GM12878	blood:	n/a	n/a
28	BHLHE40	chr2:33497047-33497454	GM12878	blood:	n/a	n/a
29	ATF2	chr2:33496929-33497573	GM12878	blood:	n/a	n/a
30	SP1	chr2:33497090-33497514	GM12878	blood:	n/a	n/a
31	POU2F2	chr2:33497065-33497431	GM12891	blood:	n/a	chr2:33497214-33497227 chr2:33497209-33497230
32	MEF2C	chr2:33497055-33497550	GM12878	blood:	n/a	n/a
33	PAX5	chr2:33497017-33497482	GM12878	blood:	n/a	n/a
34	IKZF1	chr2:33497084-33497484	GM12878	blood:	n/a	n/a
35	SP1	chr2:33497025-33497505	GM12878	blood:	n/a	n/a
36	NFIC	chr2:33496950-33497579	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:33496051..33497746-chr2:33589877..33592347,2	MCF-7	breast:
2	chr2:33491437..33494514-chr2:33496533..33499773,3	K562	blood:

Variant related genes	Relation type
LTBP1	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12468099	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13034772	0.83[ASN][1000 genomes]
rs2123769	0.92[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs3731575	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3769531	0.86[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3769535	0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3769536	0.82[CHD][hapmap]
rs3816479	0.92[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3820913	0.80[CEU][hapmap];0.92[EUR][1000 genomes]
rs6756709	0.85[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs870858	0.92[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	nsv873791	chr2:33489975-33586776	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33466400-33497400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:33466600-33500800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:33472000-33516600	Weak transcription	Psoas Muscle	Psoas
4	chr2:33487000-33509800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:33487800-33502400	Weak transcription	Brain Anterior Caudate	brain
6	chr2:33490000-33499400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:33490600-33515600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:33491800-33502000	Weak transcription	Brain Angular Gyrus	brain
9	chr2:33491800-33504400	Weak transcription	Colonic Mucosa	Colon
10	chr2:33492000-33515800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:33492200-33501000	Weak transcription	Placenta	Placenta
12	chr2:33492200-33516600	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:33492200-33516600	Weak transcription	Brain Substantia Nigra	brain
14	chr2:33492400-33497200	Weak transcription	Right Ventricle	heart
15	chr2:33492400-33499400	Weak transcription	Liver	Liver
16	chr2:33492400-33499600	Weak transcription	Left Ventricle	heart
17	chr2:33492400-33500000	Weak transcription	Fetal Stomach	stomach
18	chr2:33492400-33500800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:33492400-33500800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:33492400-33500800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:33492400-33500800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:33492400-33500800	Weak transcription	Esophagus	oesophagus
23	chr2:33492400-33500800	Weak transcription	Pancreas	Pancrea
24	chr2:33492400-33501000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:33492400-33501800	Weak transcription	Lung	lung
26	chr2:33492400-33502000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:33492400-33502000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:33492400-33502000	Weak transcription	Spleen	Spleen
29	chr2:33492400-33547400	Weak transcription	Fetal Intestine Small	intestine
30	chr2:33492600-33499200	Weak transcription	NHLF	lung
31	chr2:33492600-33499800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:33492600-33499800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr2:33492600-33500800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:33492600-33502000	Weak transcription	Ovary	ovary
35	chr2:33492600-33508400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:33493400-33502000	Weak transcription	Fetal Brain Male	brain
37	chr2:33493600-33515200	Weak transcription	Fetal Lung	lung
38	chr2:33493800-33499600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr2:33493800-33503400	Weak transcription	Fetal Brain Female	brain
40	chr2:33493800-33515400	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:33494000-33497200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:33494000-33500200	Weak transcription	HUVEC	blood vessel
43	chr2:33494000-33502000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:33494200-33506200	Weak transcription	Fetal Heart	heart
45	chr2:33494200-33516000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr2:33494200-33516200	Weak transcription	Fetal Kidney	kidney
47	chr2:33494600-33497200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr2:33494600-33515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:33494800-33499600	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:33495000-33497200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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