Variant report

Variant	rs6697623
Chromosome Location	chr1:46757542-46757543
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:46753129..46754976-chr1:46756242..46758158,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12091789	0.83[EUR][1000 genomes]
rs12137934	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142240	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12146051	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019996	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4313342	0.82[EUR][1000 genomes]
rs55707872	1.00[ASN][1000 genomes]
rs6683523	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic 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 target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv470711	chr1:46660295-46810530	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6697623	NSUN4	cis	Muscle Skeletal	GTEx
rs6697623	FAAH	cis	Whole Blood	GTEx
rs6697623	NSUN4	cis	Whole Blood	GTEx
rs6697623	RP5-1109J22.1	cis	Thyroid	GTEx
rs6697623	NSUN4	Cis_1M	lymphoblastoid	RTeQTL
rs6697623	FAAH	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46715200-46764200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:46715400-46763800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:46715400-46764400	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:46715400-46765600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:46720800-46766400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:46730000-46764000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:46733600-46766200	Weak transcription	Small Intestine	intestine
8	chr1:46741600-46763400	Strong transcription	Fetal Stomach	stomach
9	chr1:46743200-46763600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:46743400-46764000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:46743400-46764000	Strong transcription	Liver	Liver
12	chr1:46743600-46763800	Strong transcription	Fetal Lung	lung
13	chr1:46744600-46761400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr1:46745200-46766400	Weak transcription	Stomach Mucosa	stomach
15	chr1:46750600-46762400	Weak transcription	Fetal Brain Male	brain
16	chr1:46750800-46764200	Weak transcription	Right Atrium	heart
17	chr1:46751400-46760800	Weak transcription	Psoas Muscle	Psoas
18	chr1:46751400-46766200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:46751800-46759000	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:46751800-46759800	Weak transcription	Brain Substantia Nigra	brain
21	chr1:46751800-46762600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:46752000-46759800	Weak transcription	Pancreas	Pancrea
23	chr1:46752000-46760600	Weak transcription	Colonic Mucosa	Colon
24	chr1:46752000-46761000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:46752000-46761000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:46752000-46761200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:46752000-46762400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:46752000-46763000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:46752000-46765000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:46752200-46758600	Weak transcription	Lung	lung
31	chr1:46752200-46759000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:46752200-46759000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr1:46752200-46759000	Weak transcription	Esophagus	oesophagus
34	chr1:46752200-46759600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr1:46752200-46759600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:46752200-46760400	Weak transcription	Right Ventricle	heart
37	chr1:46752200-46760800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:46752200-46762400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:46752200-46762600	Weak transcription	Gastric	stomach
40	chr1:46752200-46764600	Strong transcription	Fetal Muscle Trunk	muscle
41	chr1:46752400-46759000	Weak transcription	Thymus	Thymus
42	chr1:46752400-46759400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:46752400-46759800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:46752400-46760000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:46752400-46761000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr1:46752400-46761000	Weak transcription	A549	lung
47	chr1:46752400-46762400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:46752400-46764000	Strong transcription	Fetal Muscle Leg	muscle
49	chr1:46752600-46760600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:46752800-46757600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links