Variant report

Variant	rs9613940
Chromosome Location	chr22:29927598-29927599
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29926188..29928870-chr22:29931492..29933050,2	MCF-7	breast:
2	chr22:29923072..29925512-chr22:29926077..29927603,2	MCF-7	breast:
3	chr22:29927486..29930292-chr22:29933869..29936467,2	K562	blood:

Variant related genes	Relation type
ENSG00000100296	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1058642	0.89[EUR][1000 genomes]
rs11090569	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12161054	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13056992	0.89[EUR][1000 genomes]
rs1800538	0.81[EUR][1000 genomes]
rs1807506	0.81[EUR][1000 genomes]
rs2072301	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2240638	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2267147	0.87[EUR][1000 genomes]
rs2270077	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2348672	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2348677	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2348683	0.80[EUR][1000 genomes]
rs2881994	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35404981	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3815335	0.82[TSI][hapmap]
rs3940296	0.96[CEU][hapmap];0.88[JPT][hapmap]
rs4470427	0.84[EUR][1000 genomes]
rs4479529	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6006178	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67292640	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67884471	0.80[EUR][1000 genomes]
rs715490	0.96[CEU][hapmap];0.88[JPT][hapmap]
rs7292442	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs737975	1.00[CEU][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs737980	0.83[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs737981	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8142111	0.89[EUR][1000 genomes]
rs867088	0.87[EUR][1000 genomes]
rs9608781	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs9608790	0.96[CEU][hapmap];0.88[JPT][hapmap]
rs9608794	0.96[CEU][hapmap];0.88[JPT][hapmap]
rs9608799	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	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9613943	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9613956	0.88[EUR][1000 genomes]
rs9613957	0.88[EUR][1000 genomes]
rs9613958	0.85[EUR][1000 genomes]
rs9613961	0.84[EUR][1000 genomes]
rs9613963	0.82[EUR][1000 genomes]
rs9613965	0.82[EUR][1000 genomes]
rs9613970	0.96[CEU][hapmap];0.88[JPT][hapmap]
rs9613971	0.96[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs9613975	0.96[CEU][hapmap];0.88[JPT][hapmap]
rs9613984	0.96[CEU][hapmap];0.88[JPT][hapmap]
rs9613999	0.83[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs9614004	0.83[ASW][hapmap];0.91[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs9614005	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]
rs9614006	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];0.80[EUR][1000 genomes]
rs9614011	0.83[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs9614018	0.96[CEU][hapmap];0.88[JPT][hapmap]
rs999458	0.81[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9613940	NIPSNAP1	Cis_1M	lymphoblastoid	RTeQTL
rs9613940	THOC5	cis	Thyroid	GTEx
rs9613940	THOC5	cis	Artery Tibial	GTEx
rs9613940	THOC5	cis	Adipose Subcutaneous	GTEx
rs9613940	NIPSNAP1	cis	parietal	SCAN
rs9613940	NF2	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29897600-29934600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr22:29898200-29947400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:29900400-29929000	Strong transcription	Fetal Stomach	stomach
4	chr22:29900400-29949200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr22:29900800-29929000	Strong transcription	Fetal Intestine Small	intestine
6	chr22:29900800-29930600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr22:29901000-29947600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr22:29901200-29929600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr22:29901200-29941600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr22:29901200-29945600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr22:29901400-29937200	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr22:29901400-29945800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr22:29902200-29937000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr22:29902400-29930000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr22:29902400-29941200	Strong transcription	Placenta	Placenta
16	chr22:29902600-29949000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr22:29903600-29931000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr22:29904600-29927600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr22:29910000-29947800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr22:29910600-29947800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr22:29910800-29937000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr22:29911200-29938000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr22:29911200-29947000	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr22:29911400-29930400	Strong transcription	HSMM	muscle
25	chr22:29911400-29945400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr22:29913600-29949200	Weak transcription	Right Atrium	heart
27	chr22:29914000-29929600	Weak transcription	Fetal Heart	heart
28	chr22:29917800-29942400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr22:29918000-29948000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr22:29919000-29946600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr22:29919200-29941000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr22:29919200-29946600	Strong transcription	Fetal Muscle Trunk	muscle
33	chr22:29919200-29946800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr22:29919400-29927800	Strong transcription	Fetal Lung	lung
35	chr22:29919400-29928000	Strong transcription	Brain Cingulate Gyrus	brain
36	chr22:29919400-29928000	Strong transcription	Esophagus	oesophagus
37	chr22:29919400-29928000	Strong transcription	Spleen	Spleen
38	chr22:29919400-29928000	Strong transcription	A549	lung
39	chr22:29919400-29928000	Strong transcription	HMEC	breast
40	chr22:29919400-29928200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr22:29919400-29928200	Strong transcription	Brain Angular Gyrus	brain
42	chr22:29919400-29928200	Strong transcription	Brain Substantia Nigra	brain
43	chr22:29919400-29928200	Strong transcription	Left Ventricle	heart
44	chr22:29919400-29928200	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr22:29919400-29928200	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr22:29919400-29928600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr22:29919400-29928600	Strong transcription	Brain Germinal Matrix	brain
48	chr22:29919400-29929200	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr22:29919400-29929800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr22:29919400-29930000	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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