Variant report

Variant	rs4146837
Chromosome Location	chr15:93446869-93446870
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	POLR2A	chr15:93446772-93449243	PANC-1	pancreas:	n/a	n/a
2	GABPA	chr15:93446801-93448253	A549	lung:	n/a	chr15:93448005-93448014 chr15:93447633-93447642 chr15:93447665-93447674
3	POLR2A	chr15:93445798-93449703	U87	brain:	n/a	n/a
4	POLR2A	chr15:93442973-93453321	GM12878	blood:	n/a	n/a
5	STAT3	chr15:93446601-93448836	Hela-S3	cervix:	n/a	chr15:93447634-93447646 chr15:93448484-93448504 chr15:93447845-93447865 chr15:93447850-93447859 chr15:93446695-93446702 chr15:93447848-93447862 chr15:93447851-93447859 chr15:93447845-93447865 chr15:93447851-93447860
6	YY1	chr15:93446856-93447905	H1-hESC	embryonic stem cell:	n/a	chr15:93447584-93447598 chr15:93447423-93447431 chr15:93447633-93447642 chr15:93447212-93447222 chr15:93447412-93447434
7	POLR2A	chr15:93433692-93455675	K562	blood:	n/a	n/a
8	POLR2A	chr15:93446020-93448870	HepG2	liver:	n/a	n/a
9	POLR2A	chr15:93446817-93448980	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr15:93445723-93452019	IMR90	lung:	n/a	n/a
11	HEY1	chr15:93446800-93448180	HepG2	liver:	n/a	chr15:93447612-93447621 chr15:93447610-93447619
12	TEAD4	chr15:93445997-93449031	K562	blood:	n/a	n/a
13	RELA	chr15:93445931-93448073	GM12878	blood:	n/a	chr15:93447745-93447754 chr15:93447745-93447754
14	NFATC1	chr15:93446250-93448561	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:93443026-93448707	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr15:93445945-93449157	K562	blood:	n/a	n/a
17	TCF7L2	chr15:93446744-93447675	HepG2	liver:	n/a	chr15:93446939-93446955 chr15:93447508-93447522 chr15:93446940-93446954 chr15:93446942-93446951 chr15:93446939-93446955
18	BCLAF1	chr15:93446824-93448074	K562	blood:	n/a	chr15:93447601-93447610
19	ARID3A	chr15:93445678-93448097	K562	blood:	n/a	n/a
20	POLR2A	chr15:93446850-93448190	H1-hESC	embryonic stem cell:	n/a	n/a
21	YY1	chr15:93446824-93448038	SK-N-SH	brain:	n/a	chr15:93447584-93447598 chr15:93447423-93447431 chr15:93447633-93447642 chr15:93447212-93447222 chr15:93447412-93447434 chr15:93448005-93448014
22	POLR2A	chr15:93443087-93448872	MCF-7	breast:	n/a	n/a
23	HEY1	chr15:93446853-93448065	HepG2	liver:	n/a	chr15:93447612-93447621 chr15:93447610-93447619
24	CHD1	chr15:93443269-93448419	H1-hESC	embryonic stem cell:	n/a	chr15:93447634-93447644 chr15:93448003-93448013
25	POLR2A	chr15:93446840-93455881	K562	blood:	n/a	n/a
26	KAP1	chr15:93445903-93446900	K562	blood:	n/a	n/a
27	POLR2A	chr15:93445786-93453047	GM12891	blood:	n/a	n/a
28	BCLAF1	chr15:93446676-93448710	K562	blood:	n/a	chr15:93447601-93447610
29	YY1	chr15:93446867-93447906	A549	lung:	n/a	chr15:93447584-93447598 chr15:93447423-93447431 chr15:93447633-93447642 chr15:93447212-93447222 chr15:93447412-93447434
30	STAT3	chr15:93446806-93447108	MCF10A-Er-Src	breast:	n/a	n/a
31	TAF7	chr15:93446842-93448026	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr15:93442438-93449413	Hela-S3	cervix:	n/a	n/a
33	ARID3A	chr15:93446287-93447875	HepG2	liver:	n/a	n/a
34	POLR2A	chr15:93445726-93448992	GM12878	blood:	n/a	n/a
35	MAX	chr15:93446812-93448224	HCT-116	colon:	n/a	chr15:93447663-93447672 chr15:93447606-93447615
36	TAF1	chr15:93446786-93448132	A549	lung:	n/a	n/a
37	SPI1	chr15:93446229-93446887	GM12878	blood:	n/a	chr15:93446400-93446413
38	NFATC1	chr15:93445890-93448961	GM12878	blood:	n/a	n/a
39	MAX	chr15:93446826-93448809	A549	lung:	n/a	chr15:93447663-93447672 chr15:93447606-93447615
40	RELA	chr15:93445939-93448575	GM18505	blood:	n/a	chr15:93447745-93447754 chr15:93447745-93447754
41	MXI1	chr15:93442841-93449632	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr15:93445924-93448969	HepG2	liver:	n/a	n/a
43	POLR2A	chr15:93445759-93449645	U87	brain:	n/a	n/a
44	MYC	chr15:93446822-93448353	K562	blood:	n/a	chr15:93447663-93447672 chr15:93447606-93447615
45	IRF1	chr15:93446073-93450870	K562	blood:	n/a	chr15:93447265-93447279 chr15:93450726-93450735 chr15:93447970-93447984 chr15:93450727-93450736 chr15:93447545-93447554 chr15:93447632-93447646 chr15:93448001-93448015 chr15:93448087-93448100 chr15:93446787-93446799 chr15:93449105-93449119
46	POLR2A	chr15:93446756-93448953	PANC-1	pancreas:	n/a	n/a
47	SIN3AK20	chr15:93446864-93448801	MCF-7	breast:	n/a	n/a
48	ELF1	chr15:93446821-93448307	HCT-116	colon:	n/a	chr15:93447848-93447859
49	POLR2A	chr15:93445782-93450636	MCF10A-Er-Src	breast:	n/a	n/a
50	SIN3AK20	chr15:93446837-93448342	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:93377060..93379186-chr15:93444151..93447492,3	K562	blood:
2	chr14:91526593..91527163-chr15:93446473..93447260,2	NB4	blood:
3	chr15:93393520..93395102-chr15:93444710..93447228,2	K562	blood:
4	chr15:93333327..93367027-chr15:93419774..93462750,363	K562	blood:
5	chr15:93344712..93371031-chr15:93418700..93467618,365	MCF-7	breast:
6	chr15:91498274..91499230-chr15:93446602..93447366,2	Hela-S3	cervix:
7	chr15:93372787..93376736-chr15:93445833..93447508,3	K562	blood:
8	chr15:93337836..93370220-chr15:93420085..93452591,332	K562	blood:
9	chr15:93345383..93371459-chr15:93416796..93454653,318	MCF-7	breast:

Variant related genes	Relation type
MIR3175	TF binding region
CHD2	TF binding region
ENSG00000133943	Chromatin interaction
ENSG00000258527	Chromatin interaction
ENSG00000100784	Chromatin interaction
ENSG00000166965	Chromatin interaction
ENSG00000258384	Chromatin interaction
ENSG00000258922	Chromatin interaction
ENSG00000185442	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10852185	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11074119	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1143115	0.94[ASW][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12903587	0.89[ASW][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs12904071	0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12907473	0.85[EUR][1000 genomes]
rs12908968	0.89[ASW][hapmap];0.80[LWK][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1439618	0.94[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1439619	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17648415	0.82[JPT][hapmap]
rs3826037	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4146836	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer 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 miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
3	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
4	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
5	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv1047496	chr15:93412778-93475878	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
7	nsv1036560	chr15:93413594-93462163	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
8	esv1851305	chr15:93429646-93446869	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv530847	chr15:93444024-93555676	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
10	nsv917347	chr15:93444094-93586814	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4146837	CIB1	cis	cerebellum	SCAN
rs4146837	ZNF710	cis	parietal	SCAN
rs4146837	FAM174B	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93438200-93447200	Weak transcription	Spleen	Spleen
2	chr15:93442600-93449000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr15:93443000-93448200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:93443000-93448200	Active TSS	NHEK	skin
5	chr15:93443000-93448600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr15:93443200-93447200	Active TSS	HMEC	breast
7	chr15:93443200-93448000	Active TSS	Brain Substantia Nigra	brain
8	chr15:93443200-93448200	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr15:93443200-93448200	Active TSS	H9 Cell Line	embryonic stem cell
10	chr15:93443200-93448200	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr15:93443200-93448200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:93443200-93448200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr15:93443200-93448200	Active TSS	Duodenum Mucosa	Duodenum
14	chr15:93443200-93448400	Active TSS	H1 Cell Line	embryonic stem cell
15	chr15:93443200-93448400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:93443200-93448400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:93443200-93448400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:93443200-93448400	Active TSS	Brain Germinal Matrix	brain
19	chr15:93443200-93448400	Active TSS	Placenta	Placenta
20	chr15:93443200-93448400	Active TSS	Fetal Stomach	stomach
21	chr15:93443200-93448400	Active TSS	HSMM	muscle
22	chr15:93443200-93448600	Active TSS	Colonic Mucosa	Colon
23	chr15:93443200-93448800	Active TSS	Aorta	Aorta
24	chr15:93443200-93448800	Active TSS	Fetal Muscle Trunk	muscle
25	chr15:93443200-93448800	Active TSS	Ovary	ovary
26	chr15:93443200-93449200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:93443200-93449400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:93443200-93449800	Active TSS	Right Ventricle	heart
29	chr15:93443200-93450000	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr15:93443200-93450000	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr15:93443400-93448200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:93443400-93448200	Active TSS	Fetal Intestine Large	intestine
33	chr15:93443400-93448200	Active TSS	Fetal Thymus	thymus
34	chr15:93443400-93448400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr15:93443400-93448400	Active TSS	Thymus	Thymus
36	chr15:93443400-93449200	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr15:93443400-93449800	Active TSS	Psoas Muscle	Psoas
38	chr15:93443400-93450000	Active TSS	Right Atrium	heart
39	chr15:93443600-93448200	Active TSS	Stomach Mucosa	stomach
40	chr15:93443600-93448400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr15:93443600-93448400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:93443600-93448600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr15:93443600-93449200	Active TSS	Fetal Muscle Leg	muscle
44	chr15:93444000-93447400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
45	chr15:93444400-93447000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:93444400-93447200	Transcr. at gene 5' and 3'	Dnd41	blood
47	chr15:93444600-93447200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:93444600-93447200	Weak transcription	Esophagus	oesophagus
49	chr15:93444600-93447200	Weak transcription	Pancreas	Pancrea
50	chr15:93444800-93447200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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