Variant report

Variant	rs9956
Chromosome Location	chr22:32015450-32015451
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	22:32012966-32043914..22:32347255-32351014	K562	blood:
2	22:31936958-31958600..22:32012966-32043914	GM12878	blood:
3	22:32012966-32043914..22:32513817-32522138	K562	blood:
4	chr22:31999831..32002168-chr22:32013735..32015818,2	K562	blood:
5	22:31829733-31836635..22:32012966-32043914	GM12878	blood:
6	22:32012966-32043914..22:32665993-32670527	K562	blood:
7	chr22:32013812..32017033-chr22:32024155..32027288,4	MCF-7	breast:
8	chr22:32014336..32015950-chr22:32021359..32023068,2	MCF-7	breast:
9	22:31930706-31935473..22:32012966-32043914	GM12878	blood:
10	22:32012966-32043914..22:32529813-32538538	K562	blood:
11	chr22:31960988..31962788-chr22:32015387..32017206,2	K562	blood:
12	22:32012966-32043914..22:32846948-32860159	K562	blood:
13	chr22:32014846..32016763-chr22:32018159..32020204,2	MCF-7	breast:
14	chr22:32010251..32014501-chr22:32014940..32019879,7	MCF-7	breast:
15	22:32012966-32043914..22:32360288-32405313	K562	blood:

No data

Variant related genes	Relation type
ENSG00000230866	Chromatin interaction
ENSG00000234479	Chromatin interaction
ENSG00000232707	Chromatin interaction
ENSG00000184459	Chromatin interaction
ENSG00000198089	Chromatin interaction
ENSG00000241878	Chromatin interaction
ENSG00000229169	Chromatin interaction
ENSG00000240647	Chromatin interaction
ENSG00000238910	Chromatin interaction
ENSG00000184708	Chromatin interaction
ENSG00000239674	Chromatin interaction
ENSG00000224050	Chromatin interaction
ENSG00000214093	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1044085	0.82[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12170867	0.81[JPT][hapmap]
rs12171042	1.00[ASW][hapmap];0.95[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12627933	0.83[CHD][hapmap];0.94[MEX][hapmap]
rs131233	0.82[YRI][hapmap]
rs131250	0.81[MKK][hapmap]
rs140078	0.82[ASW][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.86[YRI][hapmap]
rs140081	0.82[ASW][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.86[YRI][hapmap]
rs14034	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1543416	0.94[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap]
rs2006771	0.95[LWK][hapmap];0.89[MKK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes]
rs2092905	0.82[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap]
rs2108108	0.85[MKK][hapmap]
rs2236033	0.87[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2295242	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2295251	0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2387	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs3804087	0.82[ASW][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap]
rs3818134	0.95[CEU][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap]
rs4820051	0.90[JPT][hapmap]
rs4820979	0.95[CEU][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs4820980	0.95[CEU][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap]
rs4820982	0.95[CEU][hapmap]
rs4820983	0.94[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap]
rs5749303	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs5749304	0.85[EUR][1000 genomes]
rs5749306	0.87[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap]
rs5753667	0.95[CEU][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs5753686	0.94[ASW][hapmap];0.95[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap]
rs5753691	0.84[JPT][hapmap];0.83[MEX][hapmap]
rs5753714	0.87[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs5753732	0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs5753733	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5753734	1.00[ASW][hapmap];0.95[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5994415	0.83[ASW][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs5994420	0.86[YRI][hapmap]
rs5998042	0.94[ASW][hapmap];0.95[CEU][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs5998054	0.87[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs5998069	0.82[MKK][hapmap];0.82[YRI][hapmap]
rs5998072	0.80[AMR][1000 genomes]
rs5998086	0.82[ASW][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap]
rs7287937	0.98[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs7289075	0.95[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7291918	1.00[ASW][hapmap];0.91[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs738656	0.95[CEU][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs738684	0.87[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.84[ASN][1000 genomes]
rs738702	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs760908	0.82[ASW][hapmap];0.90[MKK][hapmap];0.85[YRI][hapmap]
rs761746	0.94[ASW][hapmap];0.95[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs761747	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8141214	0.83[MKK][hapmap]
rs8461	0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv914980	chr22:31966274-32024980	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv517534	chr22:31977594-32024980	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv829176	chr22:31998223-32029556	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv1845516	chr22:32010436-32024552	Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv2830290	chr22:32011225-32057964	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9956	SFI1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31957400-32016400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr22:31976400-32019200	Weak transcription	Fetal Brain Male	brain
3	chr22:31996600-32018200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr22:31996600-32020600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr22:31998400-32015600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr22:31998600-32022000	Weak transcription	Fetal Kidney	kidney
7	chr22:32003600-32022000	Strong transcription	Dnd41	blood
8	chr22:32008000-32021200	Weak transcription	Fetal Heart	heart
9	chr22:32008000-32022600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr22:32009600-32021800	Strong transcription	Primary T cells from cord blood	blood
11	chr22:32010200-32025600	Genic enhancers	Placenta	Placenta
12	chr22:32011400-32020000	Strong transcription	Fetal Stomach	stomach
13	chr22:32011600-32018800	Strong transcription	Brain Germinal Matrix	brain
14	chr22:32012200-32018600	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr22:32012200-32019000	Strong transcription	Rectal Smooth Muscle	rectum
16	chr22:32012200-32019800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr22:32012200-32020600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr22:32012200-32022600	Strong transcription	Thymus	Thymus
19	chr22:32012400-32018200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr22:32012400-32018200	Strong transcription	Fetal Brain Female	brain
21	chr22:32012400-32019000	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr22:32012400-32020200	Strong transcription	Fetal Thymus	thymus
23	chr22:32012600-32016200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr22:32012600-32017000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr22:32012600-32018000	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr22:32012600-32018000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr22:32012600-32018200	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr22:32012600-32018400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr22:32012600-32018400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr22:32012600-32018800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr22:32012600-32019800	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr22:32012600-32020000	Strong transcription	Right Ventricle	heart
33	chr22:32012600-32020400	Strong transcription	Liver	Liver
34	chr22:32012600-32020800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr22:32012600-32022000	Weak transcription	Psoas Muscle	Psoas
36	chr22:32012600-32024400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr22:32012800-32016600	Weak transcription	HUVEC	blood vessel
38	chr22:32012800-32017200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr22:32012800-32017200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr22:32012800-32018000	Strong transcription	Pancreas	Pancrea
41	chr22:32012800-32018600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr22:32012800-32019000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr22:32012800-32019000	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr22:32012800-32019600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr22:32012800-32019800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr22:32012800-32020800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr22:32012800-32020800	Strong transcription	Lung	lung
48	chr22:32012800-32021400	Weak transcription	Right Atrium	heart
49	chr22:32012800-32021400	Strong transcription	NHLF	lung
50	chr22:32013000-32016000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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