Variant report

Variant	rs5997937
Chromosome Location	chr22:31673859-31673860
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:31667497..31670495-chr22:31671096..31674566,4	K562	blood:
2	chr22:31657582..31659264-chr22:31672801..31675797,2	MCF-7	breast:
3	chr22:31670705..31674081-chr22:31684491..31687873,4	MCF-7	breast:
4	chr22:31670909..31673998-chr22:31741262..31743913,3	MCF-7	breast:
5	chr22:31671882..31674678-chr22:31684555..31687561,3	K562	blood:
6	chr22:31671853..31673887-chr22:31677470..31679780,2	MCF-7	breast:
7	chr22:31670893..31672907-chr22:31673053..31674567,2	K562	blood:
8	chr22:31669154..31671048-chr22:31673189..31676176,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000100100	Chromatin interaction
ENSG00000213888	Chromatin interaction
ENSG00000100105	Chromatin interaction
ENSG00000182541	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1034587	0.84[ASW][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.82[YRI][hapmap]
rs11089493	1.00[CEU][hapmap];0.84[GIH][hapmap];0.96[TSI][hapmap]
rs11089495	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1123705	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs11556237	0.87[CEU][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs11703005	0.83[ASW][hapmap];0.87[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap]
rs11704156	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs11704523	0.83[ASW][hapmap];0.87[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap]
rs12157877	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs16989459	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs16989469	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2057951	1.00[CEU][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap]
rs2899161	0.94[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap]
rs3091392	0.87[CEU][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap]
rs4820972	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs5749231	0.84[ASW][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.82[YRI][hapmap]
rs5997917	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs5997921	0.94[CEU][hapmap];0.80[GIH][hapmap];0.96[TSI][hapmap]
rs5997930	0.89[ASW][hapmap];0.92[LWK][hapmap];0.92[MKK][hapmap];0.86[YRI][hapmap]
rs5997940	0.81[YRI][hapmap]
rs5997942	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap]
rs5997959	1.00[CEU][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap]
rs695455	0.87[CEU][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap]
rs695682	0.87[CEU][hapmap]
rs713619	1.00[CEU][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap]
rs7286926	1.00[CEU][hapmap]
rs7287715	0.87[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs738658	0.82[GIH][hapmap];0.94[MEX][hapmap]
rs739428	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs8143159	0.83[ASW][hapmap];0.87[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap]
rs8595	0.93[CEU][hapmap]

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	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
5	nsv962787	chr22:31672944-31674328	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5997937	SFI1	cis	cerebellum	SCAN
rs5997937	DUSP18	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31645000-31677600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr22:31650200-31675600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr22:31650200-31679200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr22:31650600-31676400	Weak transcription	Hela-S3	cervix
5	chr22:31651800-31675800	Strong transcription	HMEC	breast
6	chr22:31652800-31675800	Strong transcription	NHEK	skin
7	chr22:31652800-31679400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr22:31653800-31676200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr22:31654000-31676400	Strong transcription	Thymus	Thymus
10	chr22:31654000-31680400	Strong transcription	Lung	lung
11	chr22:31654000-31685600	Strong transcription	Fetal Stomach	stomach
12	chr22:31654200-31677200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:31654200-31680200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr22:31654200-31680400	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr22:31654400-31679600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr22:31655400-31680800	Weak transcription	K562	blood
17	chr22:31656800-31674000	Weak transcription	Brain Angular Gyrus	brain
18	chr22:31657800-31681200	Strong transcription	Adipose Nuclei	Adipose
19	chr22:31659000-31685600	Weak transcription	Psoas Muscle	Psoas
20	chr22:31659400-31678600	Strong transcription	Fetal Muscle Leg	muscle
21	chr22:31661400-31677800	Weak transcription	A549	lung
22	chr22:31661600-31674200	Strong transcription	Liver	Liver
23	chr22:31661800-31677000	Strong transcription	Spleen	Spleen
24	chr22:31661800-31677600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr22:31665600-31679400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr22:31665800-31678800	Strong transcription	Fetal Muscle Trunk	muscle
27	chr22:31666000-31682600	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr22:31666000-31684200	Strong transcription	Aorta	Aorta
29	chr22:31666200-31675200	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr22:31667000-31676200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr22:31667000-31676400	Strong transcription	Fetal Lung	lung
32	chr22:31667000-31684600	Weak transcription	Right Atrium	heart
33	chr22:31667400-31676800	Strong transcription	Osteobl	bone
34	chr22:31667400-31677200	Strong transcription	Dnd41	blood
35	chr22:31668000-31675000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr22:31668400-31674000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr22:31668400-31681200	Strong transcription	NHLF	lung
38	chr22:31668600-31674400	Strong transcription	NHDF-Ad	bronchial
39	chr22:31668800-31675400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr22:31668800-31680400	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr22:31669000-31675800	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr22:31669000-31676000	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr22:31669000-31676200	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr22:31669000-31676600	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr22:31669000-31678800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr22:31669000-31679400	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr22:31669000-31680200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr22:31669000-31680400	Strong transcription	Brain Anterior Caudate	brain
49	chr22:31669000-31682200	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr22:31669000-31682400	Strong transcription	Monocytes-CD14+_RO01746	blood

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