Variant report

Variant	rs10758789
Chromosome Location	chr9:6431091-6431092
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6430526..6432813-chr9:6434801..6436562,2	K562	blood:

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10115362	0.86[ASN][1000 genomes]
rs10115883	0.81[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs10122116	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs10124572	0.89[ASN][1000 genomes]
rs10733529	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739098	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10739099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10739100	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10739102	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10758783	0.85[ASN][1000 genomes]
rs10758784	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10758785	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10758786	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10758787	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10758788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10758790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10758791	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10758792	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10815428	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs10815435	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10975579	0.89[ASN][1000 genomes]
rs10975582	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10975583	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10975585	0.94[ASN][1000 genomes]
rs10975595	0.88[CEU][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.89[ASN][1000 genomes]
rs10975605	0.81[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs1156747	1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs11790625	0.91[ASN][1000 genomes]
rs11791651	0.81[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs11795355	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs12346455	0.83[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs12347573	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs12351293	0.89[ASN][1000 genomes]
rs12376117	0.85[ASN][1000 genomes]
rs13283381	0.87[CHB][hapmap];0.94[CHD][hapmap];0.84[TSI][hapmap]
rs13291472	0.82[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap]
rs13292799	0.92[ASN][1000 genomes]
rs13298500	0.87[CHB][hapmap];0.94[CHD][hapmap]
rs13440427	0.85[ASN][1000 genomes]
rs1381035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1381036	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1381037	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16924328	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs16924562	0.81[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs16924591	0.86[ASN][1000 genomes]
rs16924624	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs16924626	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs16924631	0.87[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs16924634	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs1824537	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1870696	0.81[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs1903419	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2065074	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2065075	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2169283	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2169286	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs2381444	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs33962342	0.81[CHB][hapmap]
rs3739654	0.83[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.84[TSI][hapmap];0.85[ASN][1000 genomes]
rs380674	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs394137	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs414107	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4380997	0.82[ASN][1000 genomes]
rs4384035	0.87[ASN][1000 genomes]
rs452135	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4556138	0.84[ASN][1000 genomes]
rs4740844	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[ASN][1000 genomes]
rs4740845	0.98[ASN][1000 genomes]
rs4742199	0.96[ASN][1000 genomes]
rs4742201	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742202	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742204	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs504698	0.86[ASN][1000 genomes]
rs530722	0.85[ASN][1000 genomes]
rs55960819	0.88[ASN][1000 genomes]
rs56218473	0.94[ASN][1000 genomes]
rs56396114	0.89[ASN][1000 genomes]
rs56939673	0.90[ASN][1000 genomes]
rs569866	0.85[ASN][1000 genomes]
rs6477086	0.82[ASN][1000 genomes]
rs6477087	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.87[TSI][hapmap]
rs67852216	0.86[ASN][1000 genomes]
rs7027302	0.88[ASN][1000 genomes]
rs7029772	0.87[CHB][hapmap]
rs7033940	0.89[ASN][1000 genomes]
rs73401679	0.87[ASN][1000 genomes]
rs7852539	0.88[CEU][hapmap];0.84[JPT][hapmap]
rs7853059	0.87[ASN][1000 genomes]
rs7853834	0.87[ASN][1000 genomes]
rs7857628	1.00[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs7860427	0.86[ASN][1000 genomes]
rs7860966	0.93[ASN][1000 genomes]
rs7861073	0.93[ASN][1000 genomes]
rs7861559	0.93[ASN][1000 genomes]
rs7865955	1.00[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs7871134	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][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	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv892160	chr9:6364449-6506038	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv892161	chr9:6364449-6523056	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10758789	IL33	cis	parietal	SCAN
rs10758789	PDCD1LG2	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6414600-6439400	Weak transcription	Colonic Mucosa	Colon
2	chr9:6414600-6449000	Weak transcription	Gastric	stomach
3	chr9:6414600-6449200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:6414600-6451800	Weak transcription	Esophagus	oesophagus
5	chr9:6414600-6477800	Weak transcription	Placenta	Placenta
6	chr9:6415400-6434000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr9:6415600-6441200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:6415600-6471400	Weak transcription	Aorta	Aorta
9	chr9:6415800-6442800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr9:6416000-6438400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:6416400-6449200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr9:6417400-6434400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:6417600-6437800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr9:6417800-6440000	Weak transcription	Fetal Brain Female	brain
15	chr9:6418000-6438200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr9:6419000-6437000	Weak transcription	Fetal Brain Male	brain
17	chr9:6419200-6433800	Weak transcription	Brain Substantia Nigra	brain
18	chr9:6419200-6437800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr9:6419400-6432200	Weak transcription	Brain Anterior Caudate	brain
20	chr9:6419400-6437400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr9:6421400-6449400	Weak transcription	Liver	Liver
22	chr9:6422200-6454000	Weak transcription	Fetal Lung	lung
23	chr9:6422800-6434000	Weak transcription	Fetal Muscle Leg	muscle
24	chr9:6422800-6434200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:6422800-6446400	Weak transcription	Brain Germinal Matrix	brain
26	chr9:6422800-6449200	Weak transcription	Pancreas	Pancrea
27	chr9:6423400-6440800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr9:6423800-6434000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr9:6425400-6433800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr9:6425800-6434000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr9:6426000-6433600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr9:6426200-6434000	Weak transcription	Fetal Intestine Large	intestine
33	chr9:6426200-6439800	Weak transcription	NHLF	lung
34	chr9:6426400-6436600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr9:6426600-6431200	Weak transcription	HSMMtube	muscle
36	chr9:6426600-6433200	Weak transcription	A549	lung
37	chr9:6427600-6433800	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr9:6427800-6431600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:6427800-6432800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr9:6427800-6433600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr9:6428000-6432000	Enhancers	Osteobl	bone
42	chr9:6428000-6432800	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr9:6428200-6431400	Weak transcription	NHEK	skin
44	chr9:6428200-6434400	Weak transcription	HepG2	liver
45	chr9:6428200-6443200	Weak transcription	Fetal Kidney	kidney
46	chr9:6428400-6432800	Enhancers	Primary T cells from cord blood	blood
47	chr9:6428400-6433800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr9:6428400-6433800	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr9:6428600-6431400	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr9:6428600-6431600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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