Variant report

Variant	rs3767163
Chromosome Location	chr1:86121895-86121896
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86114750..86117708-chr1:86118928..86121953,3	MCF-7	breast:
2	chr1:86117515..86119531-chr1:86121414..86124189,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10158408	0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10493773	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[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]
rs10493774	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11161649	0.88[CEU][hapmap]
rs12061951	0.84[YRI][hapmap]
rs12067749	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12075929	0.92[CEU][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes]
rs12564080	0.88[CEU][hapmap]
rs12722770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739713	0.88[CEU][hapmap]
rs12751296	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12754358	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17394091	0.82[AFR][1000 genomes]
rs17398175	1.00[ASW][hapmap];0.94[CHD][hapmap];0.82[LWK][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17398321	0.84[ASN][1000 genomes]
rs2069208	0.88[CEU][hapmap]
rs2274738	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34746573	0.82[AFR][1000 genomes]
rs414618	0.81[CEU][hapmap]
rs55654440	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6576784	0.88[CEU][hapmap]
rs6667672	0.83[AMR][1000 genomes]
rs6697548	0.87[AMR][1000 genomes]
rs6698578	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7354850	0.85[ASN][1000 genomes]
rs7523292	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers 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	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3767163	ZNHIT6	cis	Adipose Subcutaneous	GTEx
rs3767163	C1orf52	cis	cerebellum	SCAN
rs3767163	C1orf181	Cis_1M	lymphoblastoid	RTeQTL
rs3767163	LOC339524	cis	parietal	SCAN
rs3767163	ZNHIT6	cis	lymphoblastoid	seeQTL
rs3767163	DNASE2B	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86095400-86134800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:86103400-86173000	Weak transcription	Pancreas	Pancrea
3	chr1:86103600-86141200	Weak transcription	Thymus	Thymus
4	chr1:86103600-86142200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:86103600-86145400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:86103600-86145600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:86103600-86157400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:86103600-86172600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:86103600-86172600	Weak transcription	Gastric	stomach
10	chr1:86106000-86141200	Weak transcription	Lung	lung
11	chr1:86114000-86141200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:86114000-86143600	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:86114400-86142200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:86114400-86163200	Weak transcription	Esophagus	oesophagus
15	chr1:86115200-86123400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr1:86115200-86124800	Weak transcription	Brain Substantia Nigra	brain
17	chr1:86115200-86146800	Weak transcription	Psoas Muscle	Psoas
18	chr1:86115200-86167600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:86115400-86141000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:86116000-86123400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr1:86116400-86127000	Weak transcription	Fetal Kidney	kidney
22	chr1:86116400-86143600	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:86116400-86146200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:86116600-86122200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:86116600-86123600	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:86116600-86129200	Weak transcription	Aorta	Aorta
27	chr1:86116600-86142200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:86116600-86145400	Weak transcription	Fetal Stomach	stomach
29	chr1:86116800-86124600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:86117000-86165800	Weak transcription	Fetal Brain Female	brain
31	chr1:86117400-86122000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:86117400-86122400	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:86117400-86122800	Strong transcription	Dnd41	blood
34	chr1:86117400-86123200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:86117600-86172000	Weak transcription	Small Intestine	intestine
36	chr1:86117800-86122200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:86117800-86122800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:86118600-86122800	Strong transcription	Primary T cells from cord blood	blood
39	chr1:86118800-86122200	Strong transcription	Primary B cells from cord blood	blood
40	chr1:86118800-86123600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:86119200-86123400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:86119200-86133000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:86119200-86142200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr1:86119200-86142200	Weak transcription	Placenta	Placenta
45	chr1:86119400-86122600	Weak transcription	Spleen	Spleen
46	chr1:86119400-86125800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:86119400-86128800	Weak transcription	Fetal Intestine Small	intestine
48	chr1:86119400-86134000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:86119400-86135800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:86119400-86140600	Weak transcription	Duodenum Mucosa	Duodenum

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