Variant report

Variant	rs10916172
Chromosome Location	chr1:227783924-227783925
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10495277	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799429	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799438	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1080061	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10916177	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1154835	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs11805477	0.87[ASN][1000 genomes]
rs11806830	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11807529	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12120313	1.00[ASN][1000 genomes]
rs12122398	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12124325	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12126339	0.94[ASN][1000 genomes]
rs12131517	0.98[ASN][1000 genomes]
rs12133008	0.98[ASN][1000 genomes]
rs12135976	0.98[ASN][1000 genomes]
rs12137033	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138942	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12141938	0.83[ASN][1000 genomes]
rs12408514	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390400	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848036	0.87[ASN][1000 genomes]
rs1874371	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923822	1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs1951729	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2012386	0.98[ASN][1000 genomes]
rs2031134	0.92[ASN][1000 genomes]
rs2093608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2313245	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2999750	0.97[ASN][1000 genomes]
rs3010188	0.98[ASN][1000 genomes]
rs34901559	0.83[ASN][1000 genomes]
rs4306097	0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4653509	0.83[ASN][1000 genomes]
rs4653851	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4653862	0.98[ASN][1000 genomes]
rs4653864	0.97[ASN][1000 genomes]
rs4653865	0.84[ASN][1000 genomes]
rs4653867	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs55721361	0.98[ASN][1000 genomes]
rs55841672	0.87[ASN][1000 genomes]
rs56197655	0.87[ASN][1000 genomes]
rs56349581	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57346808	0.94[ASN][1000 genomes]
rs58274339	0.98[ASN][1000 genomes]
rs59336221	0.85[ASN][1000 genomes]
rs60625678	0.87[ASN][1000 genomes]
rs61322441	0.87[ASN][1000 genomes]
rs61566561	0.92[ASN][1000 genomes]
rs6426469	0.80[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6667937	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699448	0.98[ASN][1000 genomes]
rs7528010	0.97[ASN][1000 genomes]
rs9725624	0.84[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	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv2753828	chr1:227670265-227791265	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv873248	chr1:227710381-227786033	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3338615	chr1:227738421-227798486	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10916172	ZNF678	cis	lesional skin	skin_eQTL
rs10916172	ZNF678	cis	uninvolved skin	skin_eQTL
rs10916172	ZNF678	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227760200-227784600	Weak transcription	Fetal Kidney	kidney
2	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:227770600-227784400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:227771800-227790600	Weak transcription	Left Ventricle	heart
5	chr1:227774800-227790600	Weak transcription	Gastric	stomach
6	chr1:227774800-227799200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:227774800-227805000	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:227777200-227786000	Weak transcription	A549	lung
9	chr1:227777600-227790600	Weak transcription	Ovary	ovary
10	chr1:227779200-227799200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:227781200-227800800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:227781800-227784000	ZNF genes & repeats	Primary T cells from cord blood	blood
13	chr1:227782400-227785600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:227782400-227788800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:227782600-227784000	ZNF genes & repeats	Fetal Intestine Large	intestine
16	chr1:227782600-227784200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:227782600-227784200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr1:227782600-227784400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
19	chr1:227782600-227784400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
20	chr1:227782800-227784000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:227782800-227784200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr1:227782800-227785200	ZNF genes & repeats	Dnd41	blood
23	chr1:227783000-227784200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
24	chr1:227783200-227784200	ZNF genes & repeats	Fetal Intestine Small	intestine
25	chr1:227783400-227784000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:227783400-227784000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:227783400-227784000	ZNF genes & repeats	Fetal Brain Male	brain
28	chr1:227783400-227784000	ZNF genes & repeats	Fetal Stomach	stomach
29	chr1:227783400-227784000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
30	chr1:227783400-227784200	ZNF genes & repeats	Liver	Liver
31	chr1:227783400-227784200	ZNF genes & repeats	Fetal Brain Female	brain
32	chr1:227783600-227784000	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:227783600-227784000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:227783600-227784000	ZNF genes & repeats	Aorta	Aorta
35	chr1:227783600-227784000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
36	chr1:227783600-227784000	ZNF genes & repeats	Fetal Muscle Leg	muscle
37	chr1:227783600-227784000	ZNF genes & repeats	Lung	lung
38	chr1:227783600-227784000	ZNF genes & repeats	Thymus	Thymus
39	chr1:227783600-227784200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:227783600-227784200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:227783600-227784200	ZNF genes & repeats	Pancreas	Pancrea
42	chr1:227783600-227784400	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:227783800-227784200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:227783800-227784200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:227783800-227784200	ZNF genes & repeats	Duodenum Mucosa	Duodenum

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