Variant report

Variant	rs11090576
Chromosome Location	chr22:30094065-30094066
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30091150..30094109-chr22:30098424..30101093,2	K562	blood:
2	chr22:30086550..30091376-chr22:30091742..30099600,10	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1008515	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1009147	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[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];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16987914	0.82[AFR][1000 genomes]
rs17460259	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17462054	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800540	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1970776	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008880	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs2079339	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2079648	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2530678	0.90[LWK][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs2530680	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2857629	0.95[AFR][1000 genomes]
rs2857634	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs457930	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs467669	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs467768	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs4823046	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs4823048	0.83[EUR][1000 genomes]
rs5763315	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs5763347	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs5763348	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs5997506	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6006219	1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6006225	0.89[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73390944	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737979	1.00[JPT][hapmap]
rs8135737	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9625852	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
3	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
4	nsv529737	chr22:30060946-30109561	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv914963	chr22:30075052-30133579	Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv914964	chr22:30081715-30150549	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv515720	chr22:30081715-30163526	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv914965	chr22:30086144-30112226	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv914966	chr22:30088442-30138548	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11090576	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs11090576	CABIN1	cis	parietal	SCAN
rs11090576	SGSM1	cis	cerebellum	SCAN
rs11090576	SEC14L4	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30020800-30097000	Weak transcription	Stomach Mucosa	stomach
2	chr22:30054000-30094800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr22:30055400-30095200	Strong transcription	Fetal Intestine Small	intestine
4	chr22:30056000-30094800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr22:30063400-30094600	Strong transcription	Primary T cells from cord blood	blood
6	chr22:30075400-30097400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr22:30076800-30096400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr22:30077800-30096400	Weak transcription	Small Intestine	intestine
9	chr22:30079600-30097000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr22:30079600-30097400	Weak transcription	Hela-S3	cervix
11	chr22:30080000-30097000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr22:30080200-30098800	Weak transcription	GM12878-XiMat	blood
13	chr22:30081000-30096400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr22:30081200-30096400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr22:30085800-30095000	Strong transcription	Dnd41	blood
16	chr22:30085800-30096200	Weak transcription	Fetal Kidney	kidney
17	chr22:30086400-30094200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr22:30086400-30094400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr22:30086400-30095200	Strong transcription	Thymus	Thymus
20	chr22:30086400-30096600	Weak transcription	NHDF-Ad	bronchial
21	chr22:30086600-30094200	Strong transcription	Duodenum Mucosa	Duodenum
22	chr22:30086600-30094600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr22:30086600-30095000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr22:30086600-30098000	Weak transcription	Colon Smooth Muscle	Colon
25	chr22:30086800-30094400	Genic enhancers	Fetal Muscle Trunk	muscle
26	chr22:30086800-30094400	Strong transcription	NHLF	lung
27	chr22:30086800-30095000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr22:30087000-30098400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr22:30087600-30094200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr22:30088000-30095200	Strong transcription	Fetal Stomach	stomach
31	chr22:30088200-30096400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr22:30088200-30096800	Weak transcription	K562	blood
33	chr22:30088400-30094400	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr22:30088400-30094600	Strong transcription	Fetal Intestine Large	intestine
35	chr22:30088400-30096200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr22:30088400-30096400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr22:30088600-30094200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr22:30088800-30094800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr22:30088800-30095200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr22:30089000-30094200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr22:30089000-30095200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr22:30089000-30095800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr22:30089000-30096800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr22:30089200-30096200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr22:30089600-30095200	Genic enhancers	Fetal Muscle Leg	muscle
46	chr22:30089600-30098200	Weak transcription	Right Atrium	heart
47	chr22:30090400-30094200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr22:30090400-30094800	Strong transcription	Lung	lung
49	chr22:30090400-30096400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr22:30090400-30096600	Weak transcription	Rectal Mucosa Donor 29	rectum

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