Variant report

Variant	rs2232170
Chromosome Location	chr22:31537122-31537123
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	STAT1	chr22:31536436-31537172	Hela-S3	cervix:	n/a	chr22:31536898-31536906 chr22:31536902-31536914 chr22:31536896-31536907
2	TCF12	chr22:31536053-31537389	ECC-1	luminal epithelium:	n/a	chr22:31536437-31536447
3	NFIC	chr22:31536005-31537201	ECC-1	luminal epithelium:	n/a	n/a
4	EP300	chr22:31536005-31537285	ECC-1	luminal epithelium:	n/a	chr22:31536905-31536918 chr22:31536440-31536456
5	POLR2A	chr22:31537014-31537176	H1-hESC	embryonic stem cell:	n/a	n/a
6	NFIC	chr22:31536039-31537197	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr22:31535708-31537125	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:31367419..31370310-chr22:31536791..31539101,2	MCF-7	breast:
2	chr22:31534966..31537778-chr22:31554685..31557531,2	MCF-7	breast:
3	chr22:31497058..31499268-chr22:31535389..31537818,2	MCF-7	breast:
4	chr22:31491384..31493577-chr22:31536978..31538915,3	K562	blood:

Variant related genes	Relation type
PLA2G3	TF binding region
ENSG00000253352	Chromatin interaction
ENSG00000138942	Chromatin interaction
ENSG00000183963	Chromatin interaction
ENSG00000264141	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1034588	0.85[CEU][hapmap]
rs1034589	0.85[CEU][hapmap]
rs13158	0.85[CEU][hapmap]
rs16989382	0.85[YRI][hapmap]
rs1858821	0.85[CEU][hapmap]
rs2040533	0.90[CEU][hapmap]
rs2073857	0.85[CEU][hapmap]
rs2078803	0.85[CEU][hapmap]
rs2079431	0.85[CEU][hapmap]
rs2106294	0.85[CEU][hapmap]
rs2228619	0.85[CEU][hapmap]
rs2232176	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283879	0.85[CEU][hapmap]
rs2413029	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2413033	0.85[CEU][hapmap]
rs2413035	0.85[CEU][hapmap]
rs4141404	0.85[CEU][hapmap]
rs4820042	0.85[CEU][hapmap]
rs4820043	0.85[CEU][hapmap]
rs4820945	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4820946	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4820951	0.85[CEU][hapmap]
rs4820955	0.85[CEU][hapmap]
rs4820963	0.85[CEU][hapmap]
rs5749224	0.85[CEU][hapmap]
rs5749229	0.85[CEU][hapmap]
rs5753483	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5753521	0.85[CEU][hapmap]
rs5753543	0.85[CEU][hapmap]
rs5997913	0.85[CEU][hapmap]
rs715510	0.85[CEU][hapmap]
rs737684	0.85[CEU][hapmap]
rs737887	0.85[CEU][hapmap]
rs737888	0.85[CEU][hapmap]
rs9606830	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2232170	SFI1	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31520400-31538800	Weak transcription	Right Atrium	heart
2	chr22:31530400-31538400	Weak transcription	Left Ventricle	heart
3	chr22:31536000-31537200	Enhancers	Gastric	stomach
4	chr22:31536200-31537200	Bivalent Enhancer	Fetal Stomach	stomach
5	chr22:31536200-31538000	Enhancers	Stomach Mucosa	stomach
6	chr22:31536200-31540800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr22:31536400-31537200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:31536400-31537200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr22:31536400-31537200	Enhancers	Pancreas	Pancrea
10	chr22:31536400-31537400	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr22:31536400-31537800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr22:31536600-31537200	Enhancers	H1 Cell Line	embryonic stem cell
13	chr22:31536600-31537200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr22:31536600-31537200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr22:31536600-31537200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr22:31536600-31537200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr22:31536600-31537200	Enhancers	Brain Germinal Matrix	brain
18	chr22:31536600-31537400	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr22:31536600-31537600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr22:31536600-31538800	Weak transcription	Brain Anterior Caudate	brain
21	chr22:31536600-31538800	Weak transcription	Right Ventricle	heart
22	chr22:31536600-31539800	Enhancers	Esophagus	oesophagus
23	chr22:31536600-31540600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr22:31536800-31537200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr22:31536800-31537200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr22:31536800-31537200	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr22:31536800-31537200	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr22:31536800-31537400	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr22:31536800-31537600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr22:31537000-31537200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr22:31537000-31537200	Enhancers	Lung	lung
32	chr22:31537000-31537400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr22:31537000-31537400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr22:31537000-31538800	Weak transcription	Brain Cingulate Gyrus	brain

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