Variant report

Variant	rs1006396
Chromosome Location	chr22:30017000-30017001
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30013978..30015955-chr22:30016681..30018575,2	K562	blood:
2	chr22:30007746..30010687-chr22:30014931..30018872,3	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1049534	0.86[JPT][hapmap]
rs11704899	0.94[CEU][hapmap];0.90[TSI][hapmap]
rs11705569	0.87[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap]
rs16987832	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2074948	0.86[JPT][hapmap]
rs2247753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267152	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs2302141	0.86[JPT][hapmap]
rs2527336	0.87[CEU][hapmap]
rs2530656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2530658	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2530664	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2531848	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[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2531849	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs456285	0.82[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs456585	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs458196	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs460428	0.83[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs462444	0.83[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap]
rs463220	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs468254	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs468692	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs468795	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs468852	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs469363	0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap]
rs5763297	0.86[JPT][hapmap]
rs5763301	0.86[JPT][hapmap];0.82[TSI][hapmap]
rs5763303	0.86[JPT][hapmap]
rs5763305	0.94[CEU][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap]
rs5763306	0.86[JPT][hapmap]
rs7609	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs8135828	0.94[CEU][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.80[EUR][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	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1006396	THOC5	cis	Nerve Tibial	GTEx
rs1006396	NIPSNAP1	cis	Stomach	GTEx
rs1006396	THOC5	cis	Artery Tibial	GTEx
rs1006396	THOC5	cis	lung	GTEx
rs1006396	THOC5	cis	Muscle Skeletal	GTEx
rs1006396	THOC5	cis	Esophagus Muscularis	GTEx
rs1006396	THOC5	cis	Adipose Subcutaneous	GTEx
rs1006396	THOC5	cis	Artery Aorta	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30000400-30026600	Weak transcription	Gastric	stomach
2	chr22:30001000-30019400	Weak transcription	Thymus	Thymus
3	chr22:30002000-30017600	Weak transcription	Primary T cells from cord blood	blood
4	chr22:30002800-30017600	Weak transcription	Lung	lung
5	chr22:30003400-30017200	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr22:30003800-30032800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr22:30005200-30019400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr22:30005400-30017800	Weak transcription	Primary B cells from cord blood	blood
9	chr22:30006800-30019000	Weak transcription	Fetal Thymus	thymus
10	chr22:30007600-30017400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr22:30009600-30017600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr22:30011000-30017800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr22:30011800-30017000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr22:30011800-30017200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr22:30011800-30026200	Weak transcription	Fetal Stomach	stomach
16	chr22:30013000-30017600	Enhancers	HMEC	breast
17	chr22:30013000-30018400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr22:30013200-30017200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr22:30013200-30017800	Enhancers	NHLF	lung
20	chr22:30013400-30017000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr22:30013400-30018000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr22:30014000-30017800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr22:30014200-30017200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr22:30014200-30017600	Weak transcription	Ovary	ovary
25	chr22:30014200-30017800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr22:30014200-30019200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr22:30014200-30019200	Weak transcription	Psoas Muscle	Psoas
28	chr22:30014200-30021800	Weak transcription	Brain Angular Gyrus	brain
29	chr22:30014400-30017000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr22:30014400-30017800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr22:30014400-30018000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr22:30014400-30019200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr22:30014400-30085800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr22:30014600-30017800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr22:30014600-30017800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr22:30014800-30017000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr22:30014800-30017400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr22:30014800-30017600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr22:30014800-30017800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr22:30014800-30017800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr22:30014800-30017800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr22:30014800-30017800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr22:30014800-30017800	Weak transcription	Colon Smooth Muscle	Colon
44	chr22:30014800-30017800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr22:30014800-30017800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr22:30014800-30018000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr22:30014800-30018000	Weak transcription	Fetal Intestine Small	intestine
48	chr22:30014800-30018000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr22:30014800-30018200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr22:30014800-30019200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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