Variant report

Variant	rs2106294
Chromosome Location	chr22:31645759-31645760
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31627806..31629543-chr22:31645486..31647563,2	MCF-7	breast:
2	chr22:31607254..31610426-chr22:31643805..31645899,3	MCF-7	breast:
3	chr22:31643031..31646502-chr22:31653237..31655706,4	MCF-7	breast:
4	chr22:31642721..31645848-chr22:31739450..31742880,5	MCF-7	breast:
5	chr22:31642310..31646378-chr22:31653276..31655946,3	MCF-7	breast:
6	chr22:31555142..31556725-chr22:31643704..31646530,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182541	Chromatin interaction
ENSG00000264141	Chromatin interaction
ENSG00000213888	Chromatin interaction
ENSG00000138942	Chromatin interaction
ENSG00000100105	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1034588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1034589	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12152166	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13054220	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13056485	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs131205	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13158	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs1858821	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2040533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2073857	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2078803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2079431	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2228619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232170	0.85[CEU][hapmap]
rs2232176	0.85[CEU][hapmap]
rs2273249	0.95[CEU][hapmap]
rs2273251	0.95[CEU][hapmap]
rs2283879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283881	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2413032	0.85[EUR][1000 genomes]
rs2413033	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2413034	0.89[EUR][1000 genomes]
rs2413035	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2413045	1.00[MKK][hapmap]
rs2413046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2413047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2413049	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2899164	0.95[CEU][hapmap]
rs4141404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4299418	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4603880	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4820042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4820043	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4820955	1.00[CEU][hapmap]
rs4820962	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4820963	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5749224	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs5749229	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5749243	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5753500	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5753505	0.81[EUR][1000 genomes]
rs5753507	0.87[EUR][1000 genomes]
rs5753521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5753601	0.95[CEU][hapmap]
rs5753609	0.90[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs5753618	0.81[TSI][hapmap]
rs59315359	0.83[EUR][1000 genomes]
rs5997893	0.90[MEX][hapmap]
rs5997902	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5997912	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5997913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5997933	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5997939	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5997949	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71324184	0.84[EUR][1000 genomes]
rs714909	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs715510	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7285619	0.95[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap]
rs7287267	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs737684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737887	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs737888	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs738657	0.95[CEU][hapmap]
rs8135344	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8135347	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8135417	0.90[MEX][hapmap]
rs8138596	0.84[EUR][1000 genomes]
rs9606830	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9606831	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9606839	0.95[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap]
rs9609254	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9609257	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9609264	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9609265	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9609266	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9609267	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9609268	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9621235	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459871	chr22:31551160-31680624	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	nsv588893	chr22:31551160-31680624	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1067003	chr22:31558663-31697093	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1058844	chr22:31597104-31725296	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Type 2 diabetes nephropathy	21150874	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2106294	MN1	cis	parietal	SCAN
rs2106294	RHBDD3	cis	cerebellum	SCAN
rs2106294	SFI1	cis	Thyroid	GTEx
rs2106294	PISD	cis	cerebellum	SCAN
rs2106294	MGC17330	cis	multi-tissue	Pritchard
rs2106294	SFI1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31641200-31646600	Weak transcription	A549	lung
2	chr22:31641400-31649600	Weak transcription	Hela-S3	cervix
3	chr22:31642800-31648200	Enhancers	Stomach Mucosa	stomach
4	chr22:31643800-31646000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:31643800-31646600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr22:31644000-31645800	Flanking Active TSS	NH-A	brain
7	chr22:31644000-31646400	Active TSS	Brain Hippocampus Middle	brain
8	chr22:31644000-31647200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
9	chr22:31644200-31645800	Flanking Active TSS	Placenta	Placenta
10	chr22:31644200-31645800	Genic enhancers	Gastric	stomach
11	chr22:31644200-31646000	Active TSS	Fetal Kidney	kidney
12	chr22:31644200-31646000	Active TSS	Ovary	ovary
13	chr22:31644200-31646200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr22:31644200-31646200	Active TSS	HMEC	breast
15	chr22:31644200-31646200	Active TSS	HSMMtube	muscle
16	chr22:31644200-31646400	Active TSS	Esophagus	oesophagus
17	chr22:31644200-31649800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr22:31644200-31665800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr22:31644600-31645800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
20	chr22:31644600-31645800	Genic enhancers	Primary T cells fromperipheralblood	blood
21	chr22:31644600-31645800	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr22:31644600-31645800	Flanking Active TSS	NHLF	lung
23	chr22:31644600-31646400	Weak transcription	Small Intestine	intestine
24	chr22:31644600-31647000	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr22:31644600-31647600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr22:31644600-31647600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr22:31644600-31648200	Genic enhancers	Rectal Mucosa Donor 31	rectum
28	chr22:31644600-31649800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr22:31644600-31650400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr22:31644600-31654200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr22:31644600-31654200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr22:31644600-31654400	Weak transcription	K562	blood
33	chr22:31644600-31658000	Weak transcription	Psoas Muscle	Psoas
34	chr22:31644600-31668600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr22:31644800-31645800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr22:31644800-31645800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr22:31644800-31645800	Enhancers	Fetal Heart	heart
38	chr22:31644800-31646000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr22:31644800-31646200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr22:31644800-31646200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr22:31644800-31646200	Flanking Active TSS	Osteobl	bone
42	chr22:31644800-31646600	Weak transcription	Primary B cells from cord blood	blood
43	chr22:31644800-31646800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr22:31644800-31649200	Weak transcription	Primary T cells from cord blood	blood
45	chr22:31644800-31649600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr22:31644800-31650000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr22:31644800-31650000	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr22:31644800-31650200	Genic enhancers	HepG2	liver
49	chr22:31644800-31650800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr22:31644800-31654400	Weak transcription	Liver	Liver

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