Variant report

Variant	rs2290206
Chromosome Location	chr17:38640992-38640993
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	USF2	chr17:38640614-38644462	Hela-S3	cervix:	n/a	n/a
2	STAT3	chr17:38640777-38641024	MCF10A-Er-Src	breast:	n/a	chr17:38640970-38640977
3	NR3C1	chr17:38640720-38641106	A549	lung:	n/a	chr17:38641041-38641048 chr17:38640906-38640919 chr17:38640902-38640916
4	JUND	chr17:38640307-38641473	A549	lung:	n/a	n/a
5	NR3C1	chr17:38640494-38641323	A549	lung:	n/a	chr17:38641041-38641048 chr17:38640906-38640919 chr17:38640902-38640916
6	POLR2A	chr17:38637848-38650725	A549	lung:	n/a	n/a
7	NR3C1	chr17:38640519-38641243	A549	lung:	n/a	chr17:38641041-38641048 chr17:38640906-38640919 chr17:38640902-38640916
8	STAT3	chr17:38640789-38641024	MCF10A-Er-Src	breast:	n/a	chr17:38640970-38640977
9	STAT3	chr17:38640779-38641002	MCF10A-Er-Src	breast:	n/a	chr17:38640970-38640977
10	POLR2A	chr17:38639722-38641776	Hela-S3	cervix:	n/a	n/a
11	NR2F2	chr17:38640862-38641219	K562	blood:	n/a	n/a
12	POLR2A	chr17:38639013-38641604	Hela-S3	cervix:	n/a	n/a
13	BCL3	chr17:38639720-38643973	A549	lung:	n/a	n/a
14	POLR2A	chr17:38640112-38641444	A549	lung:	n/a	n/a
15	NR3C1	chr17:38640675-38641081	A549	lung:	n/a	chr17:38640902-38640916 chr17:38640906-38640919 chr17:38641041-38641048
16	NR3C1	chr17:38640661-38641197	A549	lung:	n/a	chr17:38641041-38641048 chr17:38640906-38640919 chr17:38640902-38640916
17	POLR2A	chr17:38639824-38641744	Hela-S3	cervix:	n/a	n/a
18	SIX5	chr17:38640768-38644658	A549	lung:	n/a	chr17:38642468-38642477
19	POLR2A	chr17:38638883-38645646	MCF10A-Er-Src	breast:	n/a	n/a
20	BCL3	chr17:38639648-38644407	A549	lung:	n/a	n/a
21	FOS	chr17:38640819-38641018	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr17:38640130-38641373	A549	lung:	n/a	n/a
23	TCF12	chr17:38639929-38641563	A549	lung:	n/a	n/a
24	CREB1	chr17:38640705-38641354	A549	lung:	n/a	n/a
25	POLR2A	chr17:38638947-38641454	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr17:38638060-38645729	MCF10A-Er-Src	breast:	n/a	n/a
27	NR3C1	chr17:38640468-38641204	A549	lung:	n/a	chr17:38641041-38641048 chr17:38640906-38640919 chr17:38640902-38640916

No.	Distal block	Cell Line	Cell type
1	chr17:38640900..38643857-chr17:38669358..38670867,2	MCF-7	breast:
2	chr17:38639003..38641951-chr17:38683883..38685651,2	MCF-7	breast:
3	chr17:38640893..38644463-chr17:38672113..38675330,4	MCF-7	breast:
4	chr17:38633817..38637978-chr17:38639202..38643004,3	K562	blood:
5	chr17:38640863..38643911-chr17:38644729..38647819,3	MCF-7	breast:
6	chr17:38640622..38642550-chr17:38663803..38666620,2	K562	blood:
7	chr17:38638255..38640177-chr17:38640329..38642532,3	K562	blood:
8	chr17:38640983..38649598-chr17:38652430..38659338,11	MCF-7	breast:
9	chr17:38634038..38637576-chr17:38640830..38643969,3	MCF-7	breast:
10	chr17:38639539..38641673-chr17:38677366..38679503,2	K562	blood:

Variant related genes	Relation type
TNS4	TF binding region
ENSG00000266088	Chromatin interaction
ENSG00000131746	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12942610	0.86[ASN][1000 genomes]
rs1901187	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2290207	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.80[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34377860	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34453034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34456044	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34879399	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35260012	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3764424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7214311	0.90[CEU][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8081819	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9303289	0.98[ASN][1000 genomes]

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	nsv1058185	chr17:38629339-38689908	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv908224	chr17:38638251-38651447	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2290206	UNC45B	cis	cerebellum	SCAN
rs2290206	C17orf102	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38627400-38646200	Weak transcription	Gastric	stomach
2	chr17:38632400-38641000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr17:38632800-38641000	Weak transcription	Osteobl	bone
4	chr17:38633000-38641000	Weak transcription	NHLF	lung
5	chr17:38633400-38643800	Weak transcription	Right Ventricle	heart
6	chr17:38635800-38641800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr17:38636000-38647000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr17:38636000-38648200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr17:38636000-38649600	Genic enhancers	HMEC	breast
10	chr17:38636600-38642600	Weak transcription	Right Atrium	heart
11	chr17:38636800-38642000	Genic enhancers	Hela-S3	cervix
12	chr17:38637000-38641000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr17:38637000-38643400	Enhancers	K562	blood
14	chr17:38637000-38644800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr17:38637200-38641000	Weak transcription	NH-A	brain
16	chr17:38637200-38641200	Enhancers	Primary T cells fromperipheralblood	blood
17	chr17:38637200-38642000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr17:38637400-38641000	Weak transcription	HSMM	muscle
19	chr17:38637400-38642000	Strong transcription	Placenta	Placenta
20	chr17:38637400-38642200	Weak transcription	Adipose Nuclei	Adipose
21	chr17:38637400-38642400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr17:38637400-38642800	Weak transcription	Small Intestine	intestine
23	chr17:38637400-38645600	Weak transcription	Spleen	Spleen
24	chr17:38637400-38648200	Genic enhancers	NHEK	skin
25	chr17:38637600-38641000	Weak transcription	NHDF-Ad	bronchial
26	chr17:38637600-38641400	Weak transcription	Dnd41	blood
27	chr17:38637600-38642200	Weak transcription	Fetal Thymus	thymus
28	chr17:38637600-38642600	Weak transcription	Esophagus	oesophagus
29	chr17:38638200-38642800	Weak transcription	Primary T cells from cord blood	blood
30	chr17:38638200-38646400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr17:38638400-38643200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr17:38638600-38642200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr17:38638600-38646200	Weak transcription	Colonic Mucosa	Colon
34	chr17:38638800-38642600	Weak transcription	Lung	lung
35	chr17:38638800-38646000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr17:38639200-38642600	Weak transcription	Stomach Mucosa	stomach
37	chr17:38639200-38645000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr17:38639200-38645000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr17:38639200-38645400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr17:38639200-38645400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr17:38639400-38641000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr17:38639400-38641200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr17:38639400-38643200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr17:38639400-38644400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr17:38639400-38645400	Weak transcription	Primary B cells from cord blood	blood
46	chr17:38639600-38641200	Genic enhancers	A549	lung
47	chr17:38639600-38641600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr17:38639600-38641800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr17:38639600-38644200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr17:38639800-38641000	Enhancers	Fetal Intestine Large	intestine

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