Variant report

Variant	rs1060742
Chromosome Location	chr2:20189015-20189016
allele	C/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	POLR2A	chr2:20188774-20190793	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr2:20188716-20190757	A549	lung:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
3	GTF2F1	chr2:20188987-20190060	Hela-S3	cervix:	n/a	n/a
4	FOXA1	chr2:20188541-20189089	HepG2	liver:	n/a	n/a
5	MAX	chr2:20189006-20190598	A549	lung:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
6	MYC	chr2:20188852-20190373	MCF10A-Er-Src	breast:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
7	TCF12	chr2:20188950-20190739	A549	lung:	n/a	n/a
8	MXI1	chr2:20188819-20190128	Hela-S3	cervix:	n/a	chr2:20189876-20189891 chr2:20189874-20189889
9	MAX	chr2:20188829-20190479	SK-N-SH	brain:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
10	MAFK	chr2:20188984-20190023	Hela-S3	cervix:	n/a	n/a
11	MYC	chr2:20188718-20190445	MCF10A-Er-Src	breast:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
12	MAX	chr2:20188915-20190245	H1-hESC	embryonic stem cell:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
13	CTCF	chr2:20189000-20189150	SK-N-SH_RA	brain:	n/a	n/a
14	MYC	chr2:20188953-20190035	K562	blood:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
15	FOXA1	chr2:20188586-20189127	HepG2	liver:	n/a	n/a
16	SIN3AK20	chr2:20189001-20190283	SK-N-SH	brain:	n/a	n/a
17	MYC	chr2:20188432-20190350	A549	lung:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
18	NFYA	chr2:20188971-20189422	Hela-S3	cervix:	n/a	n/a
19	MYC	chr2:20188932-20190128	K562	blood:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
20	ZNF263	chr2:20188915-20190206	HEK293-T-REx	kidney:	n/a	chr2:20189311-20189332 chr2:20189339-20189360
21	HCFC1	chr2:20188796-20191052	Hela-S3	cervix:	n/a	n/a
22	MXI1	chr2:20188713-20190387	IMR90	lung:	n/a	chr2:20189876-20189891 chr2:20189874-20189889
23	MAX	chr2:20188809-20190488	HepG2	liver:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
24	MAX	chr2:20188789-20190441	SK-N-SH	brain:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
25	NRF1	chr2:20188548-20190438	SK-N-SH	brain:	n/a	chr2:20189965-20189974 chr2:20189960-20189974 chr2:20189963-20189977 chr2:20189963-20189974
26	TAF1	chr2:20188946-20190245	H1-hESC	embryonic stem cell:	n/a	n/a
27	MXI1	chr2:20187611-20190928	SK-N-SH	brain:	n/a	chr2:20189876-20189891 chr2:20189874-20189889
28	MAX	chr2:20188898-20190266	Hela-S3	cervix:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487

No.	Distal block	Cell Line	Cell type
1	chr2:20100581..20103342-chr2:20187181..20189808,2	K562	blood:
2	chr2:20187710..20189541-chr2:20212607..20214933,2	K562	blood:
3	chr2:20187189..20189541-chr2:20212582..20214933,2	K562	blood:
4	chr2:20100581..20103350-chr2:20187181..20189808,3	K562	blood:
5	chr2:20188544..20190994-chr2:20211302..20213941,2	MCF-7	breast:
6	chr2:20187273..20189318-chr2:20295101..20297253,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227210	TF binding region
ENSG00000132031	Chromatin interaction
ENSG00000183891	Chromatin interaction
ENSG00000271991	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10169398	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10175095	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10197385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10208878	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10495701	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11096632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11888045	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11889206	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12052274	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12613209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12620863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13415707	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13421472	0.87[CEU][hapmap];0.87[JPT][hapmap]
rs1381817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16987265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2293671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2304588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs28477921	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28502265	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35957485	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62109404	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62109406	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62109413	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62109415	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62109416	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62109418	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62109419	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62109420	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109421	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6707471	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6719397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6755153	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7563410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7572167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7589478	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7594214	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006404	chr2:20167688-20216509	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1005431	chr2:20174676-20210163	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1011244	chr2:20174676-20216204	Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs1060742	TTC32	Cis_1M	lymphoblastoid	RTeQTL
rs1060742	TTC32	cis	Adipose Subcutaneous	GTEx
rs1060742	TTC32	cis	cerebellum	SCAN
rs1060742	TTC32	cis	parietal	SCAN
rs1060742	TTC32	cis	Thyroid	GTEx
rs1060742	TTC32	cis	Stomach	GTEx
rs1060742	LOC130502	cis	multi-tissue	Pritchard
rs1060742	MYCN	cis	parietal	SCAN
rs1060742	TTC32	cis	Heart Left Ventricle	GTEx
rs1060742	TTC32	cis	Esophagus Mucosa	GTEx
rs1060742	ARHGAP32	trans	lymphoblastoid	seeQTL
rs1060742	TTC32	cis	Esophagus Muscularis	GTEx
rs1060742	TTC32	cis	lung	GTEx
rs1060742	TTC32	cis	multi-tissue	Pritchard
rs1060742	TTC32	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20128400-20189200	Weak transcription	Small Intestine	intestine
2	chr2:20174200-20189400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:20174400-20189200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:20174800-20189200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr2:20185000-20189200	Weak transcription	Spleen	Spleen
6	chr2:20185200-20189200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:20185200-20189200	Weak transcription	Esophagus	oesophagus
8	chr2:20185200-20189400	Weak transcription	Lung	lung
9	chr2:20187600-20189200	Enhancers	Primary B cells from peripheral blood	blood
10	chr2:20187800-20189200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:20187800-20189200	Flanking Active TSS	Hela-S3	cervix
12	chr2:20188000-20189200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:20188000-20190400	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr2:20188200-20190600	Active TSS	H9 Cell Line	embryonic stem cell
15	chr2:20188400-20189200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr2:20188400-20189200	Flanking Active TSS	HMEC	breast
17	chr2:20188400-20189600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:20188400-20190600	Active TSS	Brain Cingulate Gyrus	brain
19	chr2:20188600-20189200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:20188600-20189200	Flanking Active TSS	NH-A	brain
21	chr2:20188600-20189400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:20188600-20189600	Flanking Active TSS	Osteobl	bone
23	chr2:20188600-20190000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:20188600-20190000	Active TSS	NHLF	lung
25	chr2:20188600-20190200	Active TSS	K562	blood
26	chr2:20188600-20190600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:20188600-20190800	Active TSS	H1 Cell Line	embryonic stem cell
28	chr2:20188800-20189200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr2:20188800-20189200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr2:20188800-20189200	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr2:20188800-20189200	Enhancers	Primary T cells from cord blood	blood
32	chr2:20188800-20189200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:20188800-20189200	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr2:20188800-20189200	Flanking Active TSS	Aorta	Aorta
35	chr2:20188800-20189200	Flanking Active TSS	Brain Anterior Caudate	brain
36	chr2:20188800-20189200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
37	chr2:20188800-20189200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:20188800-20189200	Flanking Active TSS	Brain Substantia Nigra	brain
39	chr2:20188800-20189200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr2:20188800-20189200	Flanking Active TSS	Fetal Brain Male	brain
41	chr2:20188800-20189200	Flanking Active TSS	Fetal Heart	heart
42	chr2:20188800-20189200	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr2:20188800-20189200	Flanking Active TSS	Rectal Smooth Muscle	rectum
44	chr2:20188800-20189200	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr2:20188800-20189200	Flanking Bivalent TSS/Enh	HepG2	liver
46	chr2:20188800-20189200	Flanking Active TSS	HSMM	muscle
47	chr2:20188800-20189400	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr2:20188800-20189400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr2:20188800-20189400	Flanking Active TSS	Brain Germinal Matrix	brain
50	chr2:20188800-20189400	Flanking Active TSS	Fetal Brain Female	brain

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