Variant report

Variant	rs2278543
Chromosome Location	chr15:73077202-73077203
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr15:73075955-73077209	HepG2	liver:	n/a	n/a
2	WRNIP1	chr15:73074942-73077820	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:73074961-73077275	GM12891	blood:	n/a	n/a
4	CTCF	chr15:73074786-73077513	A549	lung:	n/a	n/a
5	POLR2A	chr15:73074870-73077285	MCF10A-Er-Src	breast:	n/a	n/a
6	HCFC1	chr15:73074341-73077460	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr15:73075097-73077260	GM12878	blood:	n/a	n/a
8	TCF7L2	chr15:73075462-73077245	Hela-S3	cervix:	n/a	n/a
9	MXI1	chr15:73075118-73077511	GM12878	blood:	n/a	n/a
10	TCF7L2	chr15:73075734-73077298	HCT-116	colon:	n/a	n/a
11	ESRRA	chr15:73074606-73078362	GM12878	blood:	n/a	n/a
12	MXI1	chr15:73075529-73077502	HepG2	liver:	n/a	n/a
13	REST	chr15:73075211-73077345	H1-neurons	neurons:	n/a	n/a
14	RAD21	chr15:73074914-73077453	SK-N-SH	brain:	n/a	n/a
15	MAZ	chr15:73074762-73078225	IMR90	lung:	n/a	chr15:73077887-73077896
16	SIX5	chr15:73075655-73077232	A549	lung:	n/a	n/a
17	JUN	chr15:73073554-73077337	K562	blood:	n/a	n/a
18	USF2	chr15:73075997-73077224	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr15:73074901-73077609	IMR90	lung:	n/a	n/a
20	REST	chr15:73075646-73077209	A549	lung:	n/a	n/a
21	CTCF	chr15:73075322-73077232	SK-N-SH	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:73075212..73078087-chr15:73342810..73345457,4	MCF-7	breast:
2	chr15:72978938..72981317-chr15:73074560..73077463,3	K562	blood:
3	chr15:73074691..73078350-chr15:73341676..73346479,5	MCF-7	breast:
4	chr15:72563468..72565339-chr15:73075771..73077281,2	MCF-7	breast:
5	chr15:72978938..72981317-chr15:73074560..73077463,2	K562	blood:
6	chr15:73023950..73025528-chr15:73074914..73077829,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BBS4-1	chr15:73075176-73077537	ENSG00000247829
2	lnc-BBS4-1	chr15:73075176-73077537	ENSG00000260898.1

No data

Variant related genes	Relation type
ADPGK-AS1	TF binding region
ADPGK	TF binding region
ENSG00000137817	Chromatin interaction
ENSG00000067141	Chromatin interaction
ENSG00000140463	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11072384	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11072387	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12439375	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12440951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12441084	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12443420	0.80[ASN][1000 genomes]
rs12592955	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12594667	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12594844	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12594938	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16957293	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17753687	0.88[CEU][hapmap]
rs2012253	0.82[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs2415166	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28398258	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28502551	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3179616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34337823	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35136341	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35958407	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3759870	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3850988	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs4776611	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4776616	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4777528	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4777529	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4777530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4777531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4777533	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4777537	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4777538	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4777540	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4777543	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4777545	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56915357	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57621041	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58600393	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59049627	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59152128	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60405894	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60601886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60674997	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61311866	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61632994	0.81[ASN][1000 genomes]
rs62017593	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62017598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62017623	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7178409	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72662112	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72737337	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs730180	0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap]
rs7495022	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7497429	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs8032586	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8033644	0.82[CHB][hapmap]

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	esv2758386	chr15:72819785-73120560	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv2760039	chr15:72819785-73120560	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv428307	chr15:72819785-73120560	Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv482512	chr15:73023099-73175952	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2278543	SENP8	cis	occipital cortex	BrainEAC

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73076400-73077400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr15:73076400-73077400	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr15:73076400-73077800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
4	chr15:73076600-73077400	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr15:73076600-73077400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr15:73076600-73077400	Flanking Active TSS	Fetal Lung	lung
7	chr15:73076600-73077400	Enhancers	Gastric	stomach
8	chr15:73076600-73077400	Enhancers	Spleen	Spleen
9	chr15:73076600-73077800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:73076800-73077400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:73076800-73077400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:73076800-73077400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr15:73076800-73077400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr15:73076800-73077400	Flanking Active TSS	Colon Smooth Muscle	Colon
15	chr15:73076800-73077400	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr15:73076800-73077400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr15:73076800-73077400	Enhancers	Small Intestine	intestine
18	chr15:73076800-73077400	Flanking Active TSS	Dnd41	blood
19	chr15:73076800-73077600	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr15:73076800-73078600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:73077000-73077400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr15:73077000-73077400	Enhancers	Primary B cells from peripheral blood	blood
23	chr15:73077000-73077400	Enhancers	Fetal Heart	heart
24	chr15:73077000-73077400	Enhancers	Fetal Intestine Large	intestine
25	chr15:73077000-73077400	Enhancers	Fetal Intestine Small	intestine
26	chr15:73077000-73077400	Enhancers	Lung	lung
27	chr15:73077000-73077400	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr15:73077000-73077400	Enhancers	Right Atrium	heart
29	chr15:73077000-73077400	Enhancers	NHEK	skin
30	chr15:73077000-73077400	Enhancers	NHLF	lung
31	chr15:73077000-73077600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr15:73077000-73077600	Enhancers	Primary B cells from cord blood	blood
33	chr15:73077000-73077600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr15:73077000-73077600	Enhancers	Aorta	Aorta
35	chr15:73077000-73077600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr15:73077000-73077600	Enhancers	Stomach Mucosa	stomach
37	chr15:73077000-73077600	Flanking Active TSS	HepG2	liver
38	chr15:73077000-73078000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr15:73077000-73078000	Enhancers	Fetal Stomach	stomach
40	chr15:73077000-73078200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr15:73077000-73078200	Enhancers	Fetal Muscle Leg	muscle
42	chr15:73077000-73078400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr15:73077000-73078400	Enhancers	Fetal Muscle Trunk	muscle
44	chr15:73077000-73078600	Enhancers	Primary hematopoietic stem cells	blood
45	chr15:73077000-73078600	Enhancers	NH-A	brain
46	chr15:73077000-73078800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:73077000-73079000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:73077000-73079600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:73077000-73079600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:73077000-73080600	Enhancers	HSMMtube	muscle

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