Variant report

Variant	rs10916481
Chromosome Location	chr1:224399944-224399945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10799507	0.82[EUR][1000 genomes]
rs10799543	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916458	0.85[EUR][1000 genomes]
rs10916462	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10916472	0.82[EUR][1000 genomes]
rs10916497	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916498	0.89[EUR][1000 genomes]
rs12082619	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12083770	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120308	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124547	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126765	0.82[EUR][1000 genomes]
rs12133599	0.82[EUR][1000 genomes]
rs12138866	0.85[EUR][1000 genomes]
rs12140137	0.85[EUR][1000 genomes]
rs12184283	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45583539	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60256604	0.82[EUR][1000 genomes]
rs6660194	0.82[EUR][1000 genomes]
rs6686449	0.85[EUR][1000 genomes]
rs68073536	0.89[EUR][1000 genomes]
rs72753956	0.82[EUR][1000 genomes]
rs72753969	0.82[EUR][1000 genomes]
rs72753994	0.82[EUR][1000 genomes]
rs72754000	0.85[EUR][1000 genomes]
rs72755905	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7514140	0.82[EUR][1000 genomes]
rs7552239	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
3	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10916481	CNIH4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224389600-224414400	Weak transcription	Fetal Brain Female	brain
2	chr1:224391600-224400000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:224391600-224400200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:224391600-224407000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:224392600-224400400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:224393600-224400200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:224393600-224400200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:224393600-224400200	Weak transcription	Gastric	stomach
9	chr1:224393600-224400400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:224393600-224400400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:224393600-224400800	Weak transcription	Right Atrium	heart
12	chr1:224393600-224401200	Weak transcription	Esophagus	oesophagus
13	chr1:224393600-224401200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:224393800-224400200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:224393800-224400200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:224393800-224400200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:224393800-224400200	Weak transcription	HSMMtube	muscle
18	chr1:224393800-224405600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:224393800-224414200	Weak transcription	Colonic Mucosa	Colon
20	chr1:224394000-224400800	Weak transcription	HSMM	muscle
21	chr1:224394000-224401200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:224394000-224414000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:224394000-224414600	Weak transcription	HMEC	breast
24	chr1:224394400-224400400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:224394400-224400600	Weak transcription	K562	blood
26	chr1:224394400-224400800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:224394600-224400200	Weak transcription	Small Intestine	intestine
28	chr1:224396800-224402200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:224397000-224401800	Enhancers	Fetal Muscle Leg	muscle
30	chr1:224397600-224402200	Enhancers	Fetal Intestine Small	intestine
31	chr1:224397600-224402400	Enhancers	Stomach Mucosa	stomach
32	chr1:224397800-224400400	Enhancers	Duodenum Mucosa	Duodenum
33	chr1:224397800-224402400	Enhancers	HepG2	liver
34	chr1:224398000-224401600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:224398000-224402400	Enhancers	Fetal Intestine Large	intestine
36	chr1:224398000-224414200	Weak transcription	Spleen	Spleen
37	chr1:224398200-224400200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:224398200-224400200	Weak transcription	Right Ventricle	heart
39	chr1:224398200-224401200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr1:224398200-224401200	Weak transcription	GM12878-XiMat	blood
41	chr1:224398400-224401400	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr1:224398600-224400200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:224398600-224400200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:224398600-224401800	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr1:224398800-224400200	Enhancers	NHEK	skin
46	chr1:224398800-224401000	Enhancers	Muscle Satellite Cultured Cells	--
47	chr1:224398800-224401400	Enhancers	Hela-S3	cervix
48	chr1:224398800-224401800	Enhancers	Placenta Amnion	Placenta Amnion
49	chr1:224399000-224400400	Enhancers	NH-A	brain
50	chr1:224399000-224400400	Enhancers	NHLF	lung

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