Variant report

Variant	rs6660194
Chromosome Location	chr1:224382535-224382536
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10799491	0.84[EUR][1000 genomes]
rs10799507	0.92[EUR][1000 genomes]
rs10799543	0.88[EUR][1000 genomes]
rs10916458	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10916462	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10916472	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916481	0.82[EUR][1000 genomes]
rs10916497	0.88[EUR][1000 genomes]
rs10916498	0.92[EUR][1000 genomes]
rs12082619	0.88[EUR][1000 genomes]
rs12083770	0.92[EUR][1000 genomes]
rs12120308	0.92[EUR][1000 genomes]
rs12124547	0.88[EUR][1000 genomes]
rs12126765	0.84[EUR][1000 genomes]
rs12126815	0.80[EUR][1000 genomes]
rs12133599	0.92[EUR][1000 genomes]
rs12138866	0.88[EUR][1000 genomes]
rs12140137	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12184283	0.88[EUR][1000 genomes]
rs45583539	0.88[EUR][1000 genomes]
rs60256604	0.84[EUR][1000 genomes]
rs6686449	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6701036	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68073536	0.92[EUR][1000 genomes]
rs72753956	0.92[EUR][1000 genomes]
rs72753969	0.92[EUR][1000 genomes]
rs72753980	0.84[EUR][1000 genomes]
rs72753994	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72754000	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72754001	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72755905	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7514140	0.92[EUR][1000 genomes]
rs7552239	0.88[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	nsv8857	chr1:224359943-224383023	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6660194	CNIH4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 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	chr1:224373000-224383600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:224373200-224392400	Weak transcription	Colonic Mucosa	Colon
8	chr1:224373400-224383600	Weak transcription	Small Intestine	intestine
9	chr1:224373400-224384400	Weak transcription	Brain Germinal Matrix	brain
10	chr1:224373400-224392400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:224373400-224392400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:224373400-224392600	Weak transcription	Psoas Muscle	Psoas
13	chr1:224373600-224392400	Weak transcription	Brain Angular Gyrus	brain
14	chr1:224373800-224384200	Weak transcription	Fetal Brain Male	brain
15	chr1:224373800-224392400	Weak transcription	Esophagus	oesophagus
16	chr1:224373800-224392400	Weak transcription	Fetal Heart	heart
17	chr1:224373800-224392400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:224374000-224384800	Weak transcription	Stomach Mucosa	stomach
19	chr1:224374000-224391000	Weak transcription	Spleen	Spleen
20	chr1:224374000-224392400	Weak transcription	Pancreas	Pancrea
21	chr1:224375000-224383000	Weak transcription	Gastric	stomach
22	chr1:224376400-224383000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:224377200-224382600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:224377200-224382600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:224377200-224383200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:224377200-224383200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:224377200-224384200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:224377400-224382600	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr1:224377400-224383200	Strong transcription	Primary T cells from cord blood	blood
30	chr1:224377400-224383200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:224377400-224383200	Strong transcription	Fetal Muscle Leg	muscle
32	chr1:224377400-224383600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:224377400-224383600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:224377400-224383600	Strong transcription	Fetal Stomach	stomach
35	chr1:224377400-224392400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:224377600-224388800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:224377800-224383600	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr1:224377800-224384000	Strong transcription	Primary B cells from cord blood	blood
39	chr1:224377800-224392400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:224379000-224383400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr1:224379400-224383200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:224379400-224383200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:224379600-224382600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:224379600-224383200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:224379600-224383200	Strong transcription	Osteobl	bone
46	chr1:224379800-224382800	Strong transcription	Right Ventricle	heart
47	chr1:224379800-224383600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:224380000-224383200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:224380200-224382600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:224380200-224383800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links