Variant report

Variant	rs10916462
Chromosome Location	chr1:224384280-224384281
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10799491	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10799507	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10799543	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916414	0.80[AMR][1000 genomes]
rs10916458	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916472	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10916481	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10916497	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916498	0.89[EUR][1000 genomes]
rs12082619	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12083770	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12120308	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12124547	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12126765	0.87[EUR][1000 genomes]
rs12126815	0.84[EUR][1000 genomes]
rs12133599	0.96[EUR][1000 genomes]
rs12138866	0.92[EUR][1000 genomes]
rs12140137	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184283	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs45583539	0.92[EUR][1000 genomes]
rs60256604	0.88[EUR][1000 genomes]
rs6660194	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6686449	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701036	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs68073536	0.89[EUR][1000 genomes]
rs72751651	0.83[EUR][1000 genomes]
rs72753956	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72753969	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72753980	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72753994	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72754000	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72754001	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72755905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514140	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7552239	0.83[AMR][1000 genomes];0.92[EUR][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
rs10916462	CNIH4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224372400-224389200	Weak transcription	Fetal Kidney	kidney
2	chr1:224372600-224391000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:224372600-224392400	Weak transcription	Ovary	ovary
4	chr1:224372600-224392600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:224372800-224392000	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:224373200-224392400	Weak transcription	Colonic Mucosa	Colon
7	chr1:224373400-224384400	Weak transcription	Brain Germinal Matrix	brain
8	chr1:224373400-224392400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:224373400-224392400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:224373400-224392600	Weak transcription	Psoas Muscle	Psoas
11	chr1:224373600-224392400	Weak transcription	Brain Angular Gyrus	brain
12	chr1:224373800-224392400	Weak transcription	Esophagus	oesophagus
13	chr1:224373800-224392400	Weak transcription	Fetal Heart	heart
14	chr1:224373800-224392400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:224374000-224384800	Weak transcription	Stomach Mucosa	stomach
16	chr1:224374000-224391000	Weak transcription	Spleen	Spleen
17	chr1:224374000-224392400	Weak transcription	Pancreas	Pancrea
18	chr1:224377400-224392400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:224377600-224388800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:224377800-224392400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:224380400-224384800	Weak transcription	NHLF	lung
22	chr1:224380400-224390800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:224380400-224391000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:224380400-224391200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:224380400-224392400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:224380600-224391000	Weak transcription	Hela-S3	cervix
27	chr1:224380600-224391200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:224381400-224384800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:224381400-224390800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:224381400-224390800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:224381400-224390800	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:224381400-224390800	Weak transcription	Fetal Lung	lung
33	chr1:224381400-224390800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:224381400-224390800	Weak transcription	HSMM	muscle
35	chr1:224381400-224390800	Weak transcription	HSMMtube	muscle
36	chr1:224381400-224391400	Weak transcription	K562	blood
37	chr1:224381400-224392000	Weak transcription	HUVEC	blood vessel
38	chr1:224381400-224392400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr1:224381400-224392400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:224381600-224384400	Weak transcription	NHEK	skin
41	chr1:224381600-224386000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:224381600-224386000	Weak transcription	HMEC	breast
43	chr1:224381600-224388800	Weak transcription	A549	lung
44	chr1:224381600-224390800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:224381600-224390800	Weak transcription	NH-A	brain
46	chr1:224381600-224391000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:224381600-224391000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:224381600-224392400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr1:224381600-224392400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:224381600-224392600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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