Variant report

Variant	rs9608799
Chromosome Location	chr22:30019726-30019727
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	chr22:30019261..30020777-chr22:30025452..30026983,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1058642	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12172347	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12484392	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13054618	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13055568	0.97[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13055746	0.97[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13056992	0.81[EUR][1000 genomes]
rs13057041	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1800538	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1807506	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2024116	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2024119	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2024121	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2072301	0.96[CEU][hapmap]
rs2240638	0.95[CEU][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap]
rs2245185	0.87[LWK][hapmap]
rs2267147	0.81[ASN][1000 genomes]
rs2348683	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348684	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2530670	0.88[LWK][hapmap]
rs34013089	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3940296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4470427	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67884471	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7287318	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs737975	0.96[CEU][hapmap]
rs737980	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap]
rs8142111	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs867088	0.81[ASN][1000 genomes]
rs9608781	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9608785	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608787	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608789	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9608794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9608798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9613940	0.83[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs9613942	0.83[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs9613956	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9613957	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9613961	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9613963	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9613965	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9613970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613977	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613978	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613979	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9613980	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9613983	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9613984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613986	0.97[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613990	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613991	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613992	0.97[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9613993	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613994	0.97[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613995	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9613996	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9613997	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9613998	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9613999	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];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9614004	1.00[ASW][hapmap];0.95[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];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614005	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]
rs9614006	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];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[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]
rs9614014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999458	0.82[JPT][hapmap];0.85[YRI][hapmap]

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	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	nsv817417	chr22:29998464-30035142	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9608799	NEFH	cis	multi-tissue	Pritchard
rs9608799	THOC5	cis	Artery Tibial	GTEx
rs9608799	NIPSNAP1	cis	parietal	SCAN
rs9608799	NF2	cis	parietal	SCAN
rs9608799	THOC5	cis	Thyroid	GTEx
rs9608799	THOC5	cis	Adipose Subcutaneous	GTEx
rs9608799	NIPSNAP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30000400-30026600	Weak transcription	Gastric	stomach
2	chr22:30003800-30032800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr22:30011800-30026200	Weak transcription	Fetal Stomach	stomach
4	chr22:30014200-30021800	Weak transcription	Brain Angular Gyrus	brain
5	chr22:30014400-30085800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr22:30014800-30020400	Weak transcription	Stomach Mucosa	stomach
7	chr22:30014800-30032000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:30015000-30021800	Weak transcription	Fetal Lung	lung
9	chr22:30015400-30026400	Weak transcription	Brain Anterior Caudate	brain
10	chr22:30016000-30020600	Enhancers	Placenta	Placenta
11	chr22:30016000-30023200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr22:30016400-30021400	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr22:30017000-30020800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr22:30017000-30021000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr22:30017200-30020600	Enhancers	Primary B cells from peripheral blood	blood
16	chr22:30017200-30022000	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr22:30017600-30019800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr22:30017600-30022000	Enhancers	Primary T cells from cord blood	blood
19	chr22:30017800-30020600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr22:30017800-30020800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr22:30017800-30020800	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr22:30017800-30021000	Enhancers	Primary B cells from cord blood	blood
23	chr22:30017800-30022200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr22:30018000-30020400	Weak transcription	Liver	Liver
25	chr22:30018000-30021800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr22:30018000-30022200	Weak transcription	Ovary	ovary
27	chr22:30018000-30026400	Weak transcription	Right Atrium	heart
28	chr22:30018000-30069200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr22:30018200-30021200	Enhancers	Osteobl	bone
30	chr22:30018200-30021400	Enhancers	NH-A	brain
31	chr22:30018200-30022000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr22:30018200-30023000	Enhancers	Hela-S3	cervix
33	chr22:30018200-30023200	Enhancers	HSMM	muscle
34	chr22:30018200-30024400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr22:30018200-30024600	Enhancers	HMEC	breast
36	chr22:30018400-30019800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr22:30018400-30021200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr22:30018400-30021200	Weak transcription	Fetal Kidney	kidney
39	chr22:30018400-30021400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr22:30018400-30022200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr22:30018400-30023800	Enhancers	HSMMtube	muscle
42	chr22:30018400-30025000	Weak transcription	Fetal Intestine Small	intestine
43	chr22:30018400-30025800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr22:30018400-30033400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr22:30018600-30020400	Weak transcription	Fetal Heart	heart
46	chr22:30018600-30020600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr22:30018600-30021200	Enhancers	Muscle Satellite Cultured Cells	--
48	chr22:30018600-30021400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr22:30018600-30021600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr22:30018600-30021800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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