Variant report

Variant	rs2007668
Chromosome Location	chr22:29908154-29908155
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr22:29908154-29908437	HepG2	liver:	n/a	n/a
2	POLR2A	chr22:29908100-29908176	K562	blood:	n/a	n/a
3	MAFK	chr22:29908150-29908443	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:29907835..29909461-chr22:29910820..29913528,2	MCF-7	breast:
2	chr22:29907526..29909424-chr22:29918736..29921432,2	MCF-7	breast:
3	chr22:29907918..29910292-chr22:29913329..29915343,2	MCF-7	breast:

Variant related genes	Relation type
THOC5	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs2052023	0.80[EUR][1000 genomes]
rs2079647	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2283860	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];0.98[ASN][1000 genomes]
rs2527334	0.93[JPT][hapmap]
rs2527335	0.93[JPT][hapmap]
rs2530661	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2530662	0.93[JPT][hapmap]
rs2531844	0.82[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs2857638	0.93[JPT][hapmap]
rs2857643	0.93[JPT][hapmap]
rs2857647	0.93[JPT][hapmap]
rs456300	0.81[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs465938	0.89[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs467812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs468150	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs468217	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs468221	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs468851	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs468902	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs468986	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5763294	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763302	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5763304	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5763378	0.93[JPT][hapmap]
rs6006179	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];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6361	0.81[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6519793	0.93[JPT][hapmap]
rs695399	0.87[EUR][1000 genomes]
rs737976	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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8140060	0.86[JPT][hapmap]
rs9613968	0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs9613976	0.82[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2007668	NIPSNAP1	cis	parietal	SCAN
rs2007668	THOC5	cis	cerebellum	SCAN
rs2007668	PITPNB	cis	cerebellum	SCAN
rs2007668	NIPSNAP1	cis	cerebellum	SCAN
rs2007668	CRYBB3	cis	parietal	SCAN
rs2007668	THOC5	cis	parietal	SCAN
rs2007668	NIPSNAP1	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29894600-29914800	Weak transcription	Hela-S3	cervix
2	chr22:29895800-29916800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr22:29897600-29934600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr22:29898200-29947400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:29898400-29911400	Weak transcription	Fetal Kidney	kidney
6	chr22:29899800-29909600	Strong transcription	Primary T cells from cord blood	blood
7	chr22:29900400-29913200	Weak transcription	Fetal Heart	heart
8	chr22:29900400-29929000	Strong transcription	Fetal Stomach	stomach
9	chr22:29900400-29949200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr22:29900600-29918000	Strong transcription	Fetal Thymus	thymus
11	chr22:29900800-29908400	Strong transcription	Brain Germinal Matrix	brain
12	chr22:29900800-29909000	Strong transcription	Fetal Brain Female	brain
13	chr22:29900800-29909600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr22:29900800-29909800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr22:29900800-29918000	Strong transcription	Fetal Muscle Leg	muscle
16	chr22:29900800-29929000	Strong transcription	Fetal Intestine Small	intestine
17	chr22:29900800-29930600	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr22:29901000-29908600	Strong transcription	Left Ventricle	heart
19	chr22:29901000-29908800	Strong transcription	Thymus	Thymus
20	chr22:29901000-29909000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr22:29901000-29909200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr22:29901000-29918000	Strong transcription	Fetal Intestine Large	intestine
23	chr22:29901000-29918400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr22:29901000-29947600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr22:29901200-29908800	Strong transcription	HSMM	muscle
26	chr22:29901200-29908800	Strong transcription	NHEK	skin
27	chr22:29901200-29909000	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr22:29901200-29909000	Strong transcription	Liver	Liver
29	chr22:29901200-29909200	Strong transcription	Brain Hippocampus Middle	brain
30	chr22:29901200-29909800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr22:29901200-29909800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr22:29901200-29910200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr22:29901200-29913400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr22:29901200-29916600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr22:29901200-29917000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr22:29901200-29918000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr22:29901200-29925200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr22:29901200-29929600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr22:29901200-29941600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr22:29901200-29945600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr22:29901400-29908400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr22:29901400-29908400	Strong transcription	NHLF	lung
43	chr22:29901400-29909000	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr22:29901400-29909000	Strong transcription	Primary B cells from cord blood	blood
45	chr22:29901400-29909600	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr22:29901400-29909800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr22:29901400-29937200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr22:29901400-29945800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr22:29901800-29918000	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr22:29902000-29908400	Strong transcription	Sigmoid Colon	Sigmoid Colon

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