Variant report

Variant	rs12167220
Chromosome Location	chr22:31504129-31504130
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	SIN3A	chr22:31503023-31504135	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAZ	chr22:31501611-31504230	IMR90	lung:	n/a	n/a
3	RAD21	chr22:31503557-31504177	ECC-1	luminal epithelium:	n/a	chr22:31503811-31503830
4	MYC	chr22:31503050-31504161	K562	blood:	n/a	n/a
5	CTCF	chr22:31503577-31504224	MCF-7	breast:	n/a	chr22:31503810-31503828 chr22:31503813-31503826
6	EBF1	chr22:31503683-31504130	GM12878	blood:	n/a	n/a
7	POLR2A	chr22:31504106-31504137	K562	blood:	n/a	n/a
8	UBTF	chr22:31503255-31504140	K562	blood:	n/a	n/a
9	RAD21	chr22:31503374-31504319	HCT-116	colon:	n/a	chr22:31503811-31503830
10	RAD21	chr22:31503437-31504271	ECC-1	luminal epithelium:	n/a	chr22:31503811-31503830
11	KAP1	chr22:31503686-31504177	HEK293	kidney:	n/a	n/a
12	RAD21	chr22:31503375-31504259	HCT-116	colon:	n/a	chr22:31503811-31503830
13	SIN3AK20	chr22:31503332-31504178	MCF-7	breast:	n/a	n/a
14	CTCF	chr22:31503582-31504333	HCT-116	colon:	n/a	chr22:31503810-31503828 chr22:31503813-31503826
15	CTCF	chr22:31503021-31504348	SK-N-SH	brain:	n/a	chr22:31503810-31503828 chr22:31503813-31503826
16	RAD21	chr22:31503604-31504138	MCF-7	breast:	n/a	chr22:31503811-31503830
17	RAD21	chr22:31503582-31504212	MCF-7	breast:	n/a	chr22:31503811-31503830
18	BACH1	chr22:31503597-31504156	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr22:31504060-31504210	WI-38	lung:	n/a	n/a
20	RAD21	chr22:31502945-31504362	SK-N-SH	brain:	n/a	chr22:31503811-31503830
21	MXI1	chr22:31501535-31504386	IMR90	lung:	n/a	n/a
22	NRF1	chr22:31503204-31504248	SK-N-SH	brain:	n/a	chr22:31503511-31503522
23	CTCF	chr22:31503615-31504296	A549	lung:	n/a	chr22:31503810-31503828 chr22:31503813-31503826
24	SMC3	chr22:31502947-31504355	SK-N-SH	brain:	n/a	chr22:31503812-31503826
25	TAF1	chr22:31502981-31504147	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAFK	chr22:31503726-31504129	HepG2	liver:	n/a	n/a
27	CREB1	chr22:31503350-31504227	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:31500412..31502253-chr22:31504112..31506575,2	MCF-7	breast:
2	chr22:31476077..31485695-chr22:31490616..31506508,29	K562	blood:
3	chr22:31503716..31506143-chr22:31686783..31689099,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198832	TF binding region
ENSG00000235573	TF binding region
ENSG00000228839	Chromatin interaction
ENSG00000100100	Chromatin interaction
ENSG00000198832	Chromatin interaction
ENSG00000273387	Chromatin interaction
ENSG00000183963	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1004243	0.95[LWK][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs11089488	0.91[AFR][1000 genomes]
rs11089489	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703403	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11703478	0.87[AFR][1000 genomes]
rs11705137	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[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]
rs12170688	0.84[ASN][1000 genomes]
rs12330010	0.88[AFR][1000 genomes]
rs13053329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13054770	0.91[AFR][1000 genomes]
rs1807739	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017301	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413016	1.00[CHD][hapmap]
rs35657209	0.89[AFR][1000 genomes]
rs4281997	0.85[AFR][1000 genomes]
rs4820934	0.81[YRI][hapmap]
rs4820938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820939	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820941	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5753446	1.00[CHD][hapmap]
rs62236155	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs737930	0.84[MKK][hapmap];0.81[YRI][hapmap]
rs8135353	1.00[CHB][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes]
rs917208	1.00[CHD][hapmap]
rs9621184	0.81[ASW][hapmap];1.00[CHB][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes]
rs9621185	1.00[CHB][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes]
rs9621187	0.88[AFR][1000 genomes]
rs9621188	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv9896	chr22:31369204-31513933	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv829173	chr22:31450043-31543956	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv914975	chr22:31466083-31514477	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv914976	chr22:31475307-31543260	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv914977	chr22:31477563-31514477	Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv964621	chr22:31503851-31509520	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12167220	SELM	cis	parietal	SCAN
rs12167220	TBC1D10A	cis	cerebellum	SCAN
rs12167220	OSBP2	cis	parietal	SCAN
rs12167220	SFI1	cis	cerebellum	SCAN
rs12167220	MN1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31501800-31504200	Active TSS	Aorta	Aorta
2	chr22:31502600-31504200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr22:31502600-31504200	Active TSS	Esophagus	oesophagus
4	chr22:31502600-31504200	Flanking Active TSS	Fetal Muscle Trunk	muscle
5	chr22:31502600-31504200	Active TSS	Left Ventricle	heart
6	chr22:31502600-31504200	Active TSS	Ovary	ovary
7	chr22:31502600-31504200	Active TSS	Right Atrium	heart
8	chr22:31502600-31504400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr22:31502600-31504400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr22:31502800-31504200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr22:31503000-31504200	Flanking Active TSS	Primary B cells from peripheral blood	blood
12	chr22:31503000-31504200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr22:31503000-31504200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr22:31503000-31504200	Flanking Active TSS	Fetal Intestine Small	intestine
15	chr22:31503200-31504200	Active TSS	H9 Cell Line	embryonic stem cell
16	chr22:31503200-31504200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr22:31503200-31504200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr22:31503200-31504200	Active TSS	Primary T cells from cord blood	blood
19	chr22:31503200-31504200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr22:31503200-31504200	Active TSS	Right Ventricle	heart
21	chr22:31503200-31504400	Flanking Active TSS	Dnd41	blood
22	chr22:31503400-31504200	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr22:31503400-31504200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr22:31503400-31504200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr22:31503400-31504400	Enhancers	Stomach Mucosa	stomach
26	chr22:31503600-31504200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr22:31503600-31504200	Flanking Active TSS	Fetal Brain Male	brain
28	chr22:31503600-31504400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr22:31503800-31504200	Active TSS	H1 Cell Line	embryonic stem cell
30	chr22:31503800-31504200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr22:31503800-31504200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr22:31503800-31504200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr22:31503800-31504200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr22:31503800-31504200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr22:31503800-31504200	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr22:31503800-31504200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr22:31503800-31504200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr22:31503800-31504200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr22:31503800-31504200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr22:31503800-31504200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr22:31503800-31504200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr22:31503800-31504200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr22:31503800-31504200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr22:31503800-31504200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr22:31503800-31504200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr22:31503800-31504200	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr22:31503800-31504200	Flanking Active TSS	Liver	Liver
48	chr22:31503800-31504200	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr22:31503800-31504200	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr22:31503800-31504200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland

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