Variant report

Variant	rs6764769
Chromosome Location	chr3:141100280-141100281
allele	A/G
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	MTA3	chr3:141096967-141100691	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:141097527-141100475	GM12892	blood:	n/a	n/a
3	BCLAF1	chr3:141099786-141100287	GM12878	blood:	n/a	n/a
4	TBL1XR1	chr3:141098041-141100496	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:141098888-141100526	GM12892	blood:	n/a	n/a
6	MEF2A	chr3:141099732-141100282	GM12878	blood:	n/a	n/a
7	NFATC1	chr3:141099703-141100426	GM12878	blood:	n/a	n/a
8	EP300	chr3:141099606-141100535	GM12878	blood:	n/a	chr3:141100244-141100258
9	CHD1	chr3:141099677-141100494	GM12878	blood:	n/a	n/a
10	NFIC	chr3:141099366-141100389	GM12878	blood:	n/a	n/a
11	MAZ	chr3:141099765-141100370	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:141097613-141100618	GM15510	blood:	n/a	n/a
13	MXI1	chr3:141099762-141100435	GM12878	blood:	n/a	n/a
14	YY1	chr3:141099841-141100553	GM12878	blood:	n/a	chr3:141100025-141100034 chr3:141100105-141100115
15	USF2	chr3:141099845-141100321	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:141097500-141100706	GM19099	blood:	n/a	n/a
17	MTA3	chr3:141098905-141100766	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:141098806-141100583	GM12892	blood:	n/a	n/a
19	STAT1	chr3:141099944-141100384	GM12878	blood:	n/a	chr3:141100054-141100065
20	RUNX3	chr3:141099738-141100340	GM12878	blood:	n/a	n/a
21	YY1	chr3:141099813-141100327	GM12892	blood:	n/a	chr3:141100025-141100034 chr3:141100105-141100115
22	CHD2	chr3:141099158-141100476	GM12878	blood:	n/a	n/a
23	NFIC	chr3:141097480-141100402	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:141097501-141100566	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:141098858-141100794	GM12892	blood:	n/a	n/a
26	EBF1	chr3:141099821-141100396	GM12878	blood:	n/a	n/a
27	PML	chr3:141097680-141100625	GM12878	blood:	n/a	chr3:141097964-141097972 chr3:141099672-141099680
28	TBP	chr3:141097931-141100325	GM12878	blood:	n/a	n/a
29	MAX	chr3:141099809-141100367	GM12878	blood:	n/a	n/a
30	SPI1	chr3:141100063-141100351	GM12891	blood:	n/a	chr3:141100247-141100260
31	IKZF1	chr3:141099700-141100341	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:141098879-141100519	GM12878	blood:	n/a	n/a
33	POU2F2	chr3:141099725-141100387	GM12878	blood:	n/a	chr3:141100098-141100109 chr3:141100097-141100107 chr3:141100096-141100109
34	BCLAF1	chr3:141099751-141100415	GM12878	blood:	n/a	n/a
35	YY1	chr3:141099809-141100301	GM12878	blood:	n/a	chr3:141100025-141100034 chr3:141100105-141100115
36	ATF2	chr3:141099612-141100418	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:141098913-141100676	GM12878	blood:	n/a	n/a
38	STAT3	chr3:141100177-141100377	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr3:141097830-141100559	GM18951	blood:	n/a	n/a
40	FOXM1	chr3:141099513-141100432	GM12878	blood:	n/a	n/a
41	POLR2A	chr3:141097492-141100757	GM18505	blood:	n/a	n/a
42	EBF1	chr3:141098115-141100331	GM12878	blood:	n/a	n/a
43	POLR2A	chr3:141100225-141100440	GM12878	blood:	n/a	n/a
44	POLR2A	chr3:141099811-141100370	GM12878	blood:	n/a	n/a
45	WRNIP1	chr3:141099365-141100662	GM12878	blood:	n/a	n/a
46	POLR2A	chr3:141099942-141100438	U87	brain:	n/a	n/a
47	EP300	chr3:141099675-141100358	GM12878	blood:	n/a	chr3:141100244-141100258
48	RUNX3	chr3:141099694-141100442	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:141097152-141101156	GM12878	blood:	n/a	n/a
50	POLR2A	chr3:141098926-141100622	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:141025307..141027416-chr3:141098861..141100392,2	MCF-7	breast:
2	chr3:141097730..141101011-chr3:141119204..141122613,4	MCF-7	breast:
3	chr3:141100225..141102458-chr3:141109602..141112183,2	K562	blood:
4	chr3:141088231..141090050-chr3:141099495..141101974,2	K562	blood:
5	chr3:141099231..141102671-chr3:141118653..141123217,4	MCF-7	breast:
6	chr3:141085458..141090258-chr3:141094745..141101789,10	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACPL2-3	chr3:141100267-141100329	NONHSAT092427
2	lnc-ACPL2-3	chr3:141100267-141100329	NONHSAT092428
3	lnc-ACPL2-3	chr3:141100267-141100329	NONHSAT092429

Variant related genes	Relation type
ZBTB38	TF binding region
ENSG00000249540	Chromatin interaction
ENSG00000177311	Chromatin interaction
ENSG00000249417	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13068733	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13077048	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1344672	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1344674	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1346408	0.81[CEU][hapmap]
rs1582874	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1863868	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs1991431	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2871960	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4683606	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57345461	0.95[ASN][1000 genomes]
rs58473751	0.95[ASN][1000 genomes]
rs6440003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440006	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6762826	0.90[JPT][hapmap]
rs6763927	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6763931	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785012	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6802753	0.84[JPT][hapmap]
rs6808936	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs724016	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7613516	0.81[CEU][hapmap]
rs7624084	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7625643	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7632381	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7650602	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9846396	1.00[CEU][hapmap];0.94[GIH][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9853018	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9856584	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6764769	RASA2	cis	cerebellum	SCAN
rs6764769	ZBTB38	cis	cerebellum	SCAN
rs6764769	SPSB4	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141087000-141107800	Weak transcription	Pancreas	Pancrea
2	chr3:141088000-141102400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:141088000-141105200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:141088200-141101800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:141088200-141102400	Weak transcription	Fetal Kidney	kidney
6	chr3:141088400-141102400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:141088400-141107600	Weak transcription	Small Intestine	intestine
8	chr3:141089200-141101800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:141089200-141101800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:141089200-141104800	Strong transcription	Fetal Intestine Large	intestine
11	chr3:141089200-141115800	Weak transcription	Psoas Muscle	Psoas
12	chr3:141089400-141102200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:141089400-141104200	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:141089600-141102400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:141089600-141102400	Weak transcription	Fetal Brain Male	brain
16	chr3:141089600-141102400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:141089600-141105600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:141089800-141102600	Strong transcription	Fetal Intestine Small	intestine
19	chr3:141091000-141107200	Weak transcription	Liver	Liver
20	chr3:141092000-141105600	Weak transcription	Gastric	stomach
21	chr3:141092200-141102400	Strong transcription	HSMM	muscle
22	chr3:141092800-141102400	Weak transcription	Hela-S3	cervix
23	chr3:141093200-141101800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:141093600-141101600	Weak transcription	NHDF-Ad	bronchial
25	chr3:141093800-141102200	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr3:141094000-141101600	Strong transcription	Osteobl	bone
27	chr3:141094000-141101800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:141094200-141102400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:141094600-141104200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:141094800-141105600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr3:141094800-141112200	Weak transcription	Spleen	Spleen
32	chr3:141095200-141105600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:141095200-141105800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:141095400-141101000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:141095400-141102400	Weak transcription	Fetal Stomach	stomach
36	chr3:141095400-141102600	Strong transcription	Placenta	Placenta
37	chr3:141095800-141101600	Weak transcription	NHEK	skin
38	chr3:141096000-141104400	Weak transcription	Fetal Heart	heart
39	chr3:141096000-141111000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:141096200-141102400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:141096200-141102400	Weak transcription	Colonic Mucosa	Colon
42	chr3:141096200-141106400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:141096800-141102600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:141097200-141100600	Enhancers	Primary B cells from peripheral blood	blood
45	chr3:141097200-141101800	Strong transcription	NH-A	brain
46	chr3:141097200-141105600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr3:141097800-141102400	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr3:141098200-141101800	Strong transcription	A549	lung
49	chr3:141098400-141101400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:141098400-141105800	Weak transcription	Right Ventricle	heart

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