Variant report

Variant	rs2124344
Chromosome Location	chr17:17480195-17480196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17478519..17480283-chr17:17495399..17496929,2	K562	blood:
2	chr17:17480072..17482528-chr17:17493213..17495620,3	MCF-7	breast:
3	chr17:17478310..17481534-chr17:17481749..17484707,3	K562	blood:
4	chr17:17477958..17480343-chr17:17481863..17484707,3	K562	blood:

Variant related genes	Relation type
ENSG00000264666	Chromatin interaction
ENSG00000206730	Chromatin interaction
ENSG00000133027	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11078389	1.00[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11651620	0.81[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs11654842	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12948060	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1531100	0.88[CEU][hapmap]
rs4244593	0.81[CEU][hapmap]
rs4244596	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4244598	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4646340	0.81[ASW][hapmap];0.88[CEU][hapmap];0.81[GIH][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs4646341	0.81[ASW][hapmap];0.88[CEU][hapmap];0.81[GIH][hapmap];0.84[LWK][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs4646346	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4646347	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4646349	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4646350	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4646351	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4646356	0.96[CEU][hapmap]
rs4646357	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4646359	0.96[CEU][hapmap]
rs4646365	0.95[CEU][hapmap]
rs4646369	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4646370	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4646372	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4646387	0.80[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4646389	0.81[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4646390	0.81[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4646391	0.80[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4646392	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs4646394	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs4646395	0.83[ASN][1000 genomes]
rs4646402	0.81[CEU][hapmap]
rs6502603	0.80[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs7209113	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7221487	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs729974	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs729975	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs746899	0.81[CEU][hapmap]
rs747770	0.84[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs750546	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs8079427	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8080165	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8082417	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs897451	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9892560	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9893179	0.83[ASN][1000 genomes]
rs9894321	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9894588	0.80[EUR][1000 genomes]
rs9895955	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907731	chr17:17358004-17504856	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv907744	chr17:17404586-17504856	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv907747	chr17:17412032-17504856	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv470579	chr17:17424332-17493810	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
8	nsv1062052	chr17:17461050-17507199	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv543237	chr17:17461050-17507199	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv833383	chr17:17464635-17509138	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2124344	RAI1	cis	parietal	SCAN
rs2124344	SNORD49B	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17465600-17484000	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr17:17466000-17484000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr17:17468800-17482800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr17:17468800-17484000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr17:17468800-17484000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr17:17469000-17482000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr17:17469000-17494000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:17469200-17493600	Weak transcription	Thymus	Thymus
9	chr17:17469600-17483800	Weak transcription	Osteobl	bone
10	chr17:17470200-17483800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr17:17470800-17483600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr17:17471600-17482800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr17:17471600-17493600	Weak transcription	Brain Angular Gyrus	brain
14	chr17:17471800-17493600	Weak transcription	Colon Smooth Muscle	Colon
15	chr17:17472400-17493600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr17:17473600-17484000	Weak transcription	HSMMtube	muscle
17	chr17:17474200-17493600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr17:17474400-17481200	Strong transcription	Fetal Stomach	stomach
19	chr17:17474600-17493800	Weak transcription	Primary B cells from cord blood	blood
20	chr17:17474800-17493200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr17:17475000-17483200	Weak transcription	Stomach Mucosa	stomach
22	chr17:17475600-17484400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr17:17475800-17484000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr17:17476800-17480800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr17:17477000-17480600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr17:17477200-17480400	Enhancers	NHDF-Ad	bronchial
27	chr17:17477200-17480600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr17:17477800-17480200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr17:17477800-17480200	Genic enhancers	Fetal Intestine Large	intestine
30	chr17:17477800-17480400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr17:17477800-17480400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr17:17477800-17480600	Strong transcription	Dnd41	blood
33	chr17:17477800-17481000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr17:17478000-17480400	Strong transcription	Primary T cells from cord blood	blood
35	chr17:17478000-17480400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr17:17478000-17480400	Strong transcription	Fetal Brain Female	brain
37	chr17:17478000-17480400	Genic enhancers	Fetal Muscle Trunk	muscle
38	chr17:17478000-17480400	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr17:17478000-17480400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr17:17478000-17480600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr17:17478000-17480600	Strong transcription	A549	lung
42	chr17:17478000-17480800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr17:17478000-17480800	Strong transcription	HepG2	liver
44	chr17:17478200-17480200	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr17:17478200-17480200	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr17:17478200-17480200	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr17:17478200-17480400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr17:17478200-17480400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr17:17478200-17480400	Enhancers	Ovary	ovary
50	chr17:17478200-17480400	Strong transcription	Pancreas	Pancrea

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