Variant report

Variant	rs6686449
Chromosome Location	chr1:224377724-224377725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CUX1	chr1:224377686-224377798	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224376961..224379372-chr1:224517838..224520632,2	K562	blood:

Variant related genes	Relation type
DEGS1	TF binding region
ENSG00000143748	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10799491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10799507	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10799543	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs10916414	0.91[AMR][1000 genomes]
rs10916458	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916462	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916472	1.00[CHB][hapmap];0.85[YRI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10916481	0.85[EUR][1000 genomes]
rs10916497	0.92[EUR][1000 genomes]
rs10916498	0.89[EUR][1000 genomes]
rs12082619	0.92[EUR][1000 genomes]
rs12083770	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12120308	0.96[EUR][1000 genomes]
rs12124547	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12126765	0.87[EUR][1000 genomes]
rs12126815	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12133599	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12138866	0.92[EUR][1000 genomes]
rs12140137	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184283	0.92[EUR][1000 genomes]
rs45583539	0.92[EUR][1000 genomes]
rs60256604	0.88[EUR][1000 genomes]
rs6660194	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6694451	1.00[CEU][hapmap]
rs6701036	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs68073536	0.89[EUR][1000 genomes]
rs72751651	0.83[EUR][1000 genomes]
rs72753956	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72753969	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72753980	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72753994	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72754000	0.85[AFR][1000 genomes];0.91[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[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7552239	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	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
rs6686449	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	chr1:224372400-224379600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:224372400-224380200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:224372400-224381000	Weak transcription	HSMMtube	muscle
4	chr1:224372400-224389200	Weak transcription	Fetal Kidney	kidney
5	chr1:224372600-224379000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:224372600-224379600	Weak transcription	HMEC	breast
7	chr1:224372600-224380000	Weak transcription	Thymus	Thymus
8	chr1:224372600-224391000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:224372600-224392400	Weak transcription	Ovary	ovary
10	chr1:224372600-224392600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:224372800-224380000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:224372800-224380000	Weak transcription	HSMM	muscle
13	chr1:224372800-224381000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:224372800-224392000	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:224373000-224383600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:224373200-224380200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:224373200-224380200	Weak transcription	HUVEC	blood vessel
18	chr1:224373200-224380400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:224373200-224382000	Weak transcription	Brain Substantia Nigra	brain
20	chr1:224373200-224392400	Weak transcription	Colonic Mucosa	Colon
21	chr1:224373400-224378200	Strong transcription	A549	lung
22	chr1:224373400-224379600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:224373400-224379600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:224373400-224381200	Weak transcription	Aorta	Aorta
25	chr1:224373400-224383600	Weak transcription	Small Intestine	intestine
26	chr1:224373400-224384400	Weak transcription	Brain Germinal Matrix	brain
27	chr1:224373400-224392400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:224373400-224392400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:224373400-224392600	Weak transcription	Psoas Muscle	Psoas
30	chr1:224373600-224379200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:224373600-224380000	Weak transcription	Brain Anterior Caudate	brain
32	chr1:224373600-224380000	Weak transcription	NHLF	lung
33	chr1:224373600-224381000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:224373600-224381000	Weak transcription	NHDF-Ad	bronchial
35	chr1:224373600-224392400	Weak transcription	Brain Angular Gyrus	brain
36	chr1:224373800-224380000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:224373800-224380000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:224373800-224381000	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:224373800-224384200	Weak transcription	Fetal Brain Male	brain
40	chr1:224373800-224392400	Weak transcription	Esophagus	oesophagus
41	chr1:224373800-224392400	Weak transcription	Fetal Heart	heart
42	chr1:224373800-224392400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:224374000-224380000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:224374000-224380600	Weak transcription	Lung	lung
45	chr1:224374000-224384800	Weak transcription	Stomach Mucosa	stomach
46	chr1:224374000-224391000	Weak transcription	Spleen	Spleen
47	chr1:224374000-224392400	Weak transcription	Pancreas	Pancrea
48	chr1:224374200-224379800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:224374200-224380000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:224374200-224380000	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links