Variant report

Variant	rs11161645
Chromosome Location	chr1:86092872-86092873
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86042786..86044474-chr1:86092443..86094288,2	K562	blood:

Variant related genes	Relation type
ENSG00000153904	Chromatin interaction
ENSG00000272691	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1047892	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs1047893	0.86[JPT][hapmap]
rs1047895	0.93[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs10518350	0.86[JPT][hapmap]
rs10782553	0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs10873709	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10873710	0.86[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs1094359	0.92[ASN][1000 genomes]
rs11161641	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11161643	0.93[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.99[ASN][1000 genomes]
rs11578464	0.86[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.89[ASN][1000 genomes]
rs12128916	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12564080	0.86[TSI][hapmap]
rs12566746	0.86[JPT][hapmap]
rs12739713	0.80[CHD][hapmap];0.86[TSI][hapmap]
rs1539444	0.86[JPT][hapmap]
rs1764285	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1764291	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1764292	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1764299	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1775988	0.93[ASW][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs1775990	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1928626	0.99[ASN][1000 genomes]
rs2069208	0.81[CHD][hapmap];0.86[TSI][hapmap]
rs2389970	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2785081	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2995537	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs34448540	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs373787	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3753786	0.86[JPT][hapmap]
rs3767162	0.84[ASN][1000 genomes]
rs414618	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs418979	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4949915	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6576784	0.80[CHD][hapmap];0.86[TSI][hapmap]
rs6672312	0.86[JPT][hapmap]
rs6689925	0.88[ASN][1000 genomes]
rs6697535	0.86[JPT][hapmap]
rs6699497	0.83[ASN][1000 genomes]
rs709801	0.92[ASN][1000 genomes]
rs7532758	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs821379	0.84[ASN][1000 genomes]
rs821381	0.81[ASN][1000 genomes]
rs821386	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs821389	0.93[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs821393	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs821394	0.92[ASN][1000 genomes]
rs821396	0.92[ASN][1000 genomes]
rs821401	0.89[ASN][1000 genomes]
rs843969	0.92[ASN][1000 genomes]
rs952837	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9700177	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1000290	chr1:86078495-86105379	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11161645	ZNHIT6	cis	lymphoblastoid	seeQTL
rs11161645	CAPN2	trans	lymphoblastoid	seeQTL
rs11161645	C1orf181	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86079200-86094400	Weak transcription	Pancreas	Pancrea
2	chr1:86083800-86095200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:86083800-86103200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:86085800-86093200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:86087400-86094400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:86088200-86094400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:86088200-86101800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr1:86088400-86094200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:86088400-86101400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:86088400-86102000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:86088400-86103000	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:86088600-86094400	Weak transcription	Fetal Intestine Large	intestine
13	chr1:86088600-86094400	Weak transcription	Left Ventricle	heart
14	chr1:86088600-86094800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:86088600-86094800	Weak transcription	Right Ventricle	heart
16	chr1:86088600-86101800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:86088600-86103000	Weak transcription	NHEK	skin
18	chr1:86088800-86093000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:86088800-86093400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:86088800-86094200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:86088800-86094200	Weak transcription	Liver	Liver
22	chr1:86088800-86094400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:86088800-86094400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:86088800-86094400	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:86088800-86094600	Weak transcription	Fetal Intestine Small	intestine
26	chr1:86088800-86094800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:86088800-86094800	Weak transcription	Esophagus	oesophagus
28	chr1:86088800-86101000	Weak transcription	Dnd41	blood
29	chr1:86088800-86101800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:86088800-86101800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:86089200-86094200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:86089200-86094200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:86089400-86093000	Weak transcription	NHDF-Ad	bronchial
34	chr1:86089400-86093200	Weak transcription	NHLF	lung
35	chr1:86089400-86093600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:86089400-86094200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:86089400-86094400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:86089400-86094400	Weak transcription	Placenta	Placenta
39	chr1:86089400-86094600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:86089400-86094800	Weak transcription	Ovary	ovary
41	chr1:86089400-86102600	Weak transcription	GM12878-XiMat	blood
42	chr1:86089400-86103000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:86089600-86093400	Weak transcription	NH-A	brain
44	chr1:86089600-86094000	Weak transcription	Fetal Stomach	stomach
45	chr1:86089600-86094400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:86090000-86094800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:86090400-86094400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:86091200-86103200	Weak transcription	Brain Angular Gyrus	brain
49	chr1:86091800-86093200	Strong transcription	Primary B cells from cord blood	blood
50	chr1:86091800-86093200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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