Variant report

Variant	rs7220104
Chromosome Location	chr17:46024660-46024661
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11079800	0.83[MEX][hapmap]
rs11079801	0.81[CEU][hapmap]
rs11079802	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11651753	0.83[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs11652185	0.82[CEU][hapmap]
rs16949418	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs16949720	0.92[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2002136	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2325748	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs2325751	0.82[CEU][hapmap]
rs2428608	0.88[ASN][1000 genomes]
rs2525095	0.87[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2525109	0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs2525110	0.87[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs2597169	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2875735	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3764396	0.82[CEU][hapmap]
rs3764398	0.93[ASN][1000 genomes]
rs3826396	0.93[ASN][1000 genomes]
rs4793738	0.95[ASN][1000 genomes]
rs4794331	0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs57768342	0.90[ASN][1000 genomes]
rs59811700	0.81[ASN][1000 genomes]
rs61665404	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6503934	0.82[CEU][hapmap]
rs7207225	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap]
rs72823505	0.92[ASN][1000 genomes]
rs9899097	0.80[ASN][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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	esv1000014	chr17:46019228-46029457	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7220104	SP2	cis	lymphoblastoid	seeQTL
rs7220104	CALCOCO2	cis	parietal	SCAN
rs7220104	ETV4	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019600-46027000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:46019800-46024800	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr17:46019800-46025600	Weak transcription	HSMM	muscle
4	chr17:46019800-46026800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr17:46019800-46026800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr17:46019800-46026800	Weak transcription	Brain Germinal Matrix	brain
7	chr17:46019800-46026800	Weak transcription	HSMMtube	muscle
8	chr17:46019800-46027400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr17:46019800-46034200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
11	chr17:46020000-46026000	Weak transcription	Fetal Heart	heart
12	chr17:46020000-46026200	Weak transcription	Fetal Kidney	kidney
13	chr17:46020000-46026400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr17:46020000-46026400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr17:46020000-46026400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr17:46020000-46026800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr17:46020000-46026800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr17:46020000-46027000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr17:46020000-46034600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr17:46020200-46026000	Weak transcription	NHDF-Ad	bronchial
21	chr17:46020200-46026200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr17:46020200-46026200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr17:46020200-46026800	Weak transcription	HUVEC	blood vessel
24	chr17:46020600-46024800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr17:46020800-46024800	Genic enhancers	Osteobl	bone
26	chr17:46020800-46025800	Genic enhancers	HepG2	liver
27	chr17:46021000-46024800	Strong transcription	Dnd41	blood
28	chr17:46021000-46024800	Genic enhancers	GM12878-XiMat	blood
29	chr17:46021600-46026200	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr17:46021800-46024800	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr17:46021800-46024800	Genic enhancers	Fetal Muscle Leg	muscle
32	chr17:46022000-46024800	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr17:46022400-46024800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr17:46022600-46024800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
35	chr17:46022600-46024800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr17:46022800-46026200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr17:46022800-46026400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr17:46023000-46026200	Weak transcription	NH-A	brain
39	chr17:46023000-46026400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr17:46023000-46026600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr17:46023000-46026800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr17:46023200-46024800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr17:46023200-46026600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr17:46023200-46026600	Weak transcription	Fetal Brain Female	brain
45	chr17:46023200-46026800	Genic enhancers	Fetal Intestine Small	intestine
46	chr17:46023200-46030000	Genic enhancers	Fetal Intestine Large	intestine
47	chr17:46023400-46024800	Genic enhancers	Fetal Thymus	thymus
48	chr17:46023400-46024800	Genic enhancers	A549	lung
49	chr17:46023400-46025800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr17:46023400-46026000	Strong transcription	Brain Anterior Caudate	brain

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