Variant report

Variant	rs7572167
Chromosome Location	chr2:20100988-20100989
allele	A/C
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	chr2:20100859-20102249	H1-neurons	neurons:	n/a	n/a
2	ZBTB33	chr2:20100950-20102238	HepG2	liver:	n/a	chr2:20101452-20101461 chr2:20101760-20101769
3	PML	chr2:20100762-20102440	K562	blood:	n/a	n/a
4	E2F6	chr2:20100962-20101999	K562	blood:	n/a	chr2:20101080-20101089 chr2:20101865-20101872 chr2:20101081-20101088 chr2:20101080-20101092 chr2:20101081-20101088 chr2:20101081-20101088
5	POLR2A	chr2:20099750-20102696	K562	blood:	n/a	n/a
6	SIN3AK20	chr2:20100612-20102379	MCF-7	breast:	n/a	n/a
7	HA-E2F1	chr2:20100884-20102205	MCF-7	breast:	n/a	chr2:20101080-20101089 chr2:20101865-20101872 chr2:20101081-20101088 chr2:20101080-20101092 chr2:20101081-20101088 chr2:20101081-20101088
8	POLR2A	chr2:20100820-20102117	GM10847	blood:	n/a	n/a
9	BCLAF1	chr2:20100929-20102518	K562	blood:	n/a	chr2:20101437-20101450
10	POLR2A	chr2:20100927-20102350	ECC-1	luminal epithelium:	n/a	n/a
11	TEAD4	chr2:20100652-20102368	K562	blood:	n/a	chr2:20102116-20102125
12	CREB1	chr2:20100814-20102634	K562	blood:	n/a	n/a
13	RELA	chr2:20099826-20102359	GM18505	blood:	n/a	n/a
14	UBTF	chr2:20100733-20102121	K562	blood:	n/a	n/a
15	POLR2A	chr2:20100277-20102472	HepG2	liver:	n/a	n/a
16	HDAC2	chr2:20100867-20102195	MCF-7	breast:	n/a	n/a
17	POLR2A	chr2:20099768-20102525	K562	blood:	n/a	n/a
18	NRF1	chr2:20100201-20102219	SK-N-SH	brain:	n/a	chr2:20101492-20101503
19	TBP	chr2:20100683-20102328	Hela-S3	cervix:	n/a	n/a
20	CEBPB	chr2:20100761-20100988	K562	blood:	n/a	n/a
21	MAX	chr2:20100654-20102359	A549	lung:	n/a	n/a
22	CUX1	chr2:20099704-20101049	K562	blood:	n/a	n/a
23	MYC	chr2:20100821-20102455	K562	blood:	n/a	n/a
24	E2F4	chr2:20100957-20102064	K562	blood:	n/a	chr2:20101080-20101089 chr2:20101865-20101872 chr2:20101081-20101088 chr2:20101080-20101092 chr2:20101081-20101088 chr2:20101081-20101088
25	CHD1	chr2:20100641-20102509	GM12878	blood:	n/a	chr2:20101865-20101872 chr2:20101452-20101461 chr2:20101760-20101769
26	POLR2A	chr2:20100836-20102337	U87	brain:	n/a	n/a
27	CEBPB	chr2:20100678-20101096	Hela-S3	cervix:	n/a	n/a
28	YY1	chr2:20100978-20102206	A549	lung:	n/a	chr2:20101177-20101191 chr2:20101177-20101186 chr2:20101437-20101446 chr2:20101437-20101448
29	SMARCB1	chr2:20100932-20102129	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr2:20099675-20102959	MCF10A-Er-Src	breast:	n/a	n/a
31	HEY1	chr2:20100786-20102516	HepG2	liver:	n/a	n/a
32	MAX	chr2:20100936-20102180	SK-N-SH	brain:	n/a	n/a
33	SP1	chr2:20100924-20102262	A549	lung:	n/a	n/a
34	TCF12	chr2:20100558-20102431	A549	lung:	n/a	chr2:20101245-20101252 chr2:20101698-20101706
35	POLR2A	chr2:20100960-20102136	GM15510	blood:	n/a	n/a
36	REST	chr2:20100594-20102699	H1-neurons	neurons:	n/a	n/a
37	POLR2A	chr2:20100902-20102435	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr2:20100923-20102168	A549	lung:	n/a	n/a
39	TBL1XR1	chr2:20100948-20102205	K562	blood:	n/a	n/a
40	POLR2A	chr2:20100883-20102520	GM18526	blood:	n/a	n/a
41	POLR2A	chr2:20100967-20102151	A549	lung:	n/a	n/a
42	POLR2A	chr2:20100693-20102499	IMR90	lung:	n/a	n/a
43	MAX	chr2:20100899-20102178	MCF-7	breast:	n/a	n/a
44	POLR2A	chr2:20100488-20101032	GM12891	blood:	n/a	n/a
45	POLR2A	chr2:20100264-20102517	GM19099	blood:	n/a	n/a
46	POLR2A	chr2:20100844-20102620	GM12892	blood:	n/a	n/a
47	BRCA1	chr2:20100825-20102336	Hela-S3	cervix:	n/a	chr2:20101760-20101769 chr2:20101452-20101461
48	ELK1	chr2:20100981-20101274	K562	blood:	n/a	n/a
49	BCLAF1	chr2:20100921-20102155	GM12878	blood:	n/a	chr2:20101437-20101450
50	MTA3	chr2:20099867-20102592	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:20099947..20101798-chr4:35496664..35498184,2	K562	blood:
2	chr2:20099437..20102980-chr2:20547960..20551663,4	K562	blood:
3	chr2:20100443..20102205-chr4:35495184..35498163,2	MCF-7	breast:
4	chr2:20099026..20101634-chr2:20189872..20192427,2	K562	blood:
5	chr2:20068233..20072834-chr2:20097586..20102817,5	K562	blood:
6	chr2:20099721..20101368-chr2:20204158..20205910,2	K562	blood:
7	chr2:19554321..19555906-chr2:20098486..20101228,2	K562	blood:
8	chr2:20068379..20070681-chr2:20098849..20101144,2	MCF-7	breast:
9	chr2:18740138..18743092-chr2:20100674..20102788,2	MCF-7	breast:
10	chr2:20100261..20103746-chr2:20249026..20255152,7	K562	blood:
11	chr19:57791183..57791865-chr2:20100452..20101040,2	Hela-S3	cervix:
12	chr2:20066730..20071387-chr2:20098933..20103374,5	MCF-7	breast:

Variant related genes	Relation type
TTC32	TF binding region
ENSG00000271991	TF binding region
ENSG00000055917	Chromatin interaction
ENSG00000068697	Chromatin interaction
ENSG00000197714	Chromatin interaction
ENSG00000223734	Chromatin interaction
ENSG00000267871	Chromatin interaction
ENSG00000227210	Chromatin interaction
ENSG00000118965	Chromatin interaction
ENSG00000240857	Chromatin interaction
ENSG00000206665	Chromatin interaction
ENSG00000228784	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10169398	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10175095	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10197385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10208878	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10495701	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes]
rs1060742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11096632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11888045	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11889206	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12052274	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12613209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12620863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13415707	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13421472	0.88[CEU][hapmap];0.88[JPT][hapmap]
rs1381817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16987265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2293671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2304588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28477921	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28502265	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35957485	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62109404	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62109406	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62109413	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62109415	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62109416	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62109418	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62109419	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62109420	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62109421	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6707471	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6719397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6755153	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7563410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7589478	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7594214	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873712	chr2:19955245-20131079	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv873714	chr2:20019616-20113088	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
5	nsv522640	chr2:20098208-20109061	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv521619	chr2:20098208-20150817	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7572167	TTC32	cis	Lymphoblastoid	GTEx
rs7572167	TTC32	cis	Adipose Subcutaneous	GTEx
rs7572167	TTC32	cis	lung	GTEx
rs7572167	TTC32	cis	Esophagus Mucosa	GTEx
rs7572167	TTC32	cis	Thyroid	GTEx
rs7572167	TTC32	cis	multi-tissue	Pritchard
rs7572167	TTC32	Cis_1M	lymphoblastoid	RTeQTL
rs7572167	TTC32	cis	Esophagus Muscularis	GTEx
rs7572167	LOC130502	cis	multi-tissue	Pritchard
rs7572167	TTC32	cis	Stomach	GTEx
rs7572167	TTC32	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20099000-20102600	Active TSS	GM12878-XiMat	blood
2	chr2:20099000-20103000	Active TSS	K562	blood
3	chr2:20099600-20101000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:20099600-20101000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr2:20099600-20101000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:20099600-20101200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr2:20099800-20101000	Flanking Active TSS	Fetal Lung	lung
8	chr2:20099800-20101200	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr2:20099800-20101200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:20099800-20102000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:20099800-20102400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:20099800-20102600	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr2:20099800-20102600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:20099800-20102600	Active TSS	Aorta	Aorta
15	chr2:20099800-20102800	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr2:20099800-20103200	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr2:20100000-20101000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr2:20100000-20101000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:20100000-20102200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:20100000-20102200	Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr2:20100000-20102400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:20100000-20102400	Active TSS	Ovary	ovary
23	chr2:20100000-20102400	Active TSS	A549	lung
24	chr2:20100000-20102600	Active TSS	Thymus	Thymus
25	chr2:20100000-20102600	Active TSS	NHDF-Ad	bronchial
26	chr2:20100200-20101200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:20100200-20102200	Active TSS	Sigmoid Colon	Sigmoid Colon
28	chr2:20100200-20102400	Active TSS	Esophagus	oesophagus
29	chr2:20100200-20102400	Active TSS	Left Ventricle	heart
30	chr2:20100200-20102400	Active TSS	Stomach Mucosa	stomach
31	chr2:20100200-20102600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:20100200-20102600	Active TSS	Fetal Muscle Trunk	muscle
33	chr2:20100200-20102800	Active TSS	Colonic Mucosa	Colon
34	chr2:20100400-20102200	Active TSS	Rectal Smooth Muscle	rectum
35	chr2:20100400-20102400	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr2:20100400-20102400	Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr2:20100400-20102400	Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr2:20100400-20102400	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr2:20100400-20102400	Active TSS	Small Intestine	intestine
40	chr2:20100400-20102400	Bivalent/Poised TSS	HepG2	liver
41	chr2:20100400-20102400	Active TSS	HMEC	breast
42	chr2:20100400-20102600	Active TSS	H9 Cell Line	embryonic stem cell
43	chr2:20100400-20102600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:20100400-20102600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:20100400-20102600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:20100400-20102600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:20100400-20102600	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr2:20100400-20102600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr2:20100400-20102600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:20100400-20102600	Active TSS	Psoas Muscle	Psoas

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