Variant report

Variant	rs2530670
Chromosome Location	chr22:30047891-30047892
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30047107..30049570-chr22:30052178..30054357,2	K562	blood:
2	chr22:30045640..30047901-chr22:30049009..30050786,2	MCF-7	breast:
3	chr22:30036794..30038709-chr22:30046357..30049323,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1034880	0.85[JPT][hapmap]
rs1476757	0.85[JPT][hapmap]
rs2071622	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245185	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245415	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2252587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267150	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2267151	0.92[ASW][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2283863	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2527337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2530667	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2530668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2530669	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2530672	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2530673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2530675	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2530676	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2531850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857637	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857639	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857640	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2857641	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857642	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2857645	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2857648	0.89[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs2857650	0.85[JPT][hapmap]
rs2857651	0.92[ASW][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs5752953	0.83[ASN][1000 genomes]
rs5763422	0.83[ASN][1000 genomes]
rs7291645	0.84[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap]
rs737931	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs9608799	0.88[LWK][hapmap]
rs9613999	0.88[LWK][hapmap]
rs9614004	0.87[LWK][hapmap]
rs9614005	0.88[LWK][hapmap]
rs9614006	0.88[LWK][hapmap]
rs9614011	0.84[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2530670	THOC5	cis	parietal	SCAN
rs2530670	NIPSNAP1	cis	parietal	SCAN
rs2530670	PITPNB	cis	cerebellum	SCAN
rs2530670	NIPSNAP1	cis	multi-tissue	Pritchard
rs2530670	NIPSNAP1	cis	cerebellum	SCAN
rs2530670	XBP1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30014400-30085800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30018000-30069200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:30020200-30057000	Weak transcription	Psoas Muscle	Psoas
4	chr22:30020200-30064200	Weak transcription	Small Intestine	intestine
5	chr22:30020800-30097000	Weak transcription	Stomach Mucosa	stomach
6	chr22:30022200-30053400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr22:30026800-30055800	Weak transcription	Gastric	stomach
8	chr22:30027600-30057200	Weak transcription	Brain Hippocampus Middle	brain
9	chr22:30027800-30056000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr22:30029600-30053800	Weak transcription	Esophagus	oesophagus
11	chr22:30032200-30057000	Weak transcription	Colonic Mucosa	Colon
12	chr22:30032200-30070000	Weak transcription	Fetal Brain Male	brain
13	chr22:30033000-30053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr22:30034400-30060400	Weak transcription	K562	blood
15	chr22:30035400-30060800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr22:30035600-30057200	Weak transcription	Placenta	Placenta
17	chr22:30036600-30052000	Weak transcription	Brain Anterior Caudate	brain
18	chr22:30036800-30053000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr22:30037200-30064200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr22:30038200-30057000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr22:30038400-30055800	Weak transcription	Fetal Kidney	kidney
22	chr22:30038400-30060600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr22:30038800-30057000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr22:30038800-30069800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr22:30039000-30050600	Weak transcription	Brain Angular Gyrus	brain
26	chr22:30039000-30050600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr22:30039000-30051000	Weak transcription	A549	lung
28	chr22:30039000-30051200	Weak transcription	HepG2	liver
29	chr22:30039000-30053800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr22:30039000-30054000	Weak transcription	Colon Smooth Muscle	Colon
31	chr22:30039000-30054600	Weak transcription	Aorta	Aorta
32	chr22:30039000-30054800	Weak transcription	NHLF	lung
33	chr22:30039000-30068000	Weak transcription	Hela-S3	cervix
34	chr22:30039200-30050400	Weak transcription	Left Ventricle	heart
35	chr22:30039200-30051000	Weak transcription	Brain Germinal Matrix	brain
36	chr22:30039200-30051200	Weak transcription	Fetal Brain Female	brain
37	chr22:30039200-30053800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr22:30039200-30056200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr22:30040200-30048400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr22:30041400-30050200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr22:30041800-30054000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr22:30042000-30051000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr22:30042200-30050600	Weak transcription	Fetal Thymus	thymus
44	chr22:30042200-30051000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr22:30042200-30057200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr22:30042400-30051000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr22:30042400-30052600	Weak transcription	GM12878-XiMat	blood
48	chr22:30042400-30052800	Weak transcription	Primary B cells from cord blood	blood
49	chr22:30042400-30053000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr22:30042600-30051000	Weak transcription	NHDF-Ad	bronchial

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