Variant report

Variant	rs1381817
Chromosome Location	chr2:20179220-20179221
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20171001..20173873-chr2:20178005..20179964,2	K562	blood:
2	chr2:20169846..20175848-chr2:20176195..20180875,7	K562	blood:
3	chr2:20176121..20179659-chr2:20189446..20191255,3	MCF-7	breast:
4	chr2:20178212..20180946-chr2:20182651..20185069,3	K562	blood:

Variant related genes	Relation type
ENSG00000118965	Chromatin interaction
ENSG00000227210	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10169398	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10175095	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208878	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10495701	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1060742	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11096632	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[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11888045	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11889206	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12052274	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12613209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12620863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13415707	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13421472	0.87[CEU][hapmap];0.87[JPT][hapmap]
rs16987265	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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs28477921	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28502265	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35957485	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62109398	1.00[AFR][1000 genomes]
rs62109404	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62109406	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62109413	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109415	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109416	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109418	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109419	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62109421	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62109426	1.00[AFR][1000 genomes]
rs6707471	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6719397	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];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6755153	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7563410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7572167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7589478	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7594214	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006404	chr2:20167688-20216509	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1005431	chr2:20174676-20210163	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1011244	chr2:20174676-20216204	Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1067839	chr2:20177392-20180238	Strong transcription Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs1381817	TTC32	cis	Esophagus Muscularis	GTEx
rs1381817	TTC32	cis	Esophagus Mucosa	GTEx
rs1381817	ARHGAP32	trans	lymphoblastoid	seeQTL
rs1381817	TTC32	cis	Heart Left Ventricle	GTEx
rs1381817	TTC32	cis	Adipose Subcutaneous	GTEx
rs1381817	TTC32	cis	cerebellum	SCAN
rs1381817	TTC32	cis	Thyroid	GTEx
rs1381817	DDX58	trans	multi-tissue	Pritchard
rs1381817	TTC32	cis	Liver	GTEx
rs1381817	TTC32	cis	multi-tissue	Pritchard
rs1381817	TTC32	cis	lymphoblastoid	seeQTL
rs1381817	DDX58	cis	Liver	GTEx
rs1381817	TTC32	cis	parietal	SCAN
rs1381817	LOC130502	cis	multi-tissue	Pritchard
rs1381817	MYCN	cis	parietal	SCAN
rs1381817	TTC32	cis	Stomach	GTEx
rs1381817	TTC32	cis	lung	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20117600-20188400	Weak transcription	Brain Angular Gyrus	brain
2	chr2:20128400-20188400	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:20128400-20189200	Weak transcription	Small Intestine	intestine
4	chr2:20129400-20184800	Weak transcription	Esophagus	oesophagus
5	chr2:20129600-20189000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:20130200-20189000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:20130400-20188800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:20130600-20188800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:20131800-20189000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:20133600-20184800	Weak transcription	Psoas Muscle	Psoas
11	chr2:20136800-20188800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:20136800-20189000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:20138200-20188800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:20138600-20184800	Weak transcription	Aorta	Aorta
15	chr2:20145200-20188000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:20153200-20184400	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:20157800-20187200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:20160600-20181200	Strong transcription	A549	lung
19	chr2:20162400-20188200	Weak transcription	Brain Substantia Nigra	brain
20	chr2:20163200-20188800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:20164200-20187800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:20164600-20187000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:20164600-20189000	Weak transcription	Placenta	Placenta
24	chr2:20164800-20189000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:20165000-20181600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:20165000-20187000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:20165000-20188400	Weak transcription	K562	blood
28	chr2:20165400-20187600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr2:20165600-20184600	Weak transcription	Gastric	stomach
30	chr2:20165800-20179800	Weak transcription	Fetal Thymus	thymus
31	chr2:20165800-20184600	Weak transcription	Lung	lung
32	chr2:20165800-20188200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:20169000-20184800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:20169000-20188800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:20169000-20189000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:20169200-20188800	Weak transcription	Right Ventricle	heart
37	chr2:20171000-20181800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:20171000-20182200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:20171800-20187800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr2:20172000-20188800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:20172200-20180600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:20172800-20181600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:20173000-20182000	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr2:20173000-20182000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:20173200-20179400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:20173200-20180400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:20173200-20181000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:20173200-20181400	Strong transcription	HepG2	liver
49	chr2:20173200-20182000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:20173200-20182200	Strong transcription	HUES6 Cell Line	embryonic stem cell

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