Variant report

Variant	rs7623867
Chromosome Location	chr3:42621071-42621072
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:42621055-42621105	HRPEpiC	eye:	n/a
2	chr3:42621055-42621105	Caco-2	colon:	n/a
3	chr3:42621055-42621105	SAEC	small airway:	n/a
4	chr3:42621055-42621105	HCM	heart:	n/a
5	chr3:42621055-42621105	NT2-D1	testis:	n/a
6	chr3:42621055-42621105	AG09319	gingival:	n/a
7	chr3:42621055-42621105	NB4	blood:	n/a
8	chr3:42621055-42621105	HCF	heart:	n/a
9	chr3:42621055-42621105	SK-N-MC	brain:	n/a
10	chr3:42621055-42621105	ProgFib	skin:	n/a
11	chr3:42621055-42621105	Hela-S3	cervix:	n/a
12	chr3:42621055-42621105	HNPCEpiC	eye:	n/a
13	chr3:42621055-42621105	ECC-1	luminal epithelium:	n/a
14	chr3:42621055-42621105	MCF-7	breast:	n/a
15	chr3:42621055-42621105	PFSK-1	brain:	n/a
16	chr3:42621055-42621105	GM06990	blood:	n/a
17	chr3:42621055-42621105	HepG2	liver:	n/a
18	chr3:42621055-42621105	AG10803	skin:	n/a
19	chr3:42621055-42621105	SKMC	muscle:	n/a
20	chr3:42621055-42621105	ovcar-3	ovarian:	n/a
21	chr3:42621055-42621105	CMK	blood:	n/a
22	chr3:42621055-42621105	SK-N-SH	brain:	n/a
23	chr3:42621055-42621105	BJ	skin:	n/a
24	chr3:42621055-42621105	HEEpiC	esophagus:	n/a
25	chr3:42621055-42621105	K562	blood:	n/a
26	chr3:42621055-42621105	AG04449	skin:	fetal
27	chr3:42621055-42621105	HEK293	kidney:	embryo
28	chr3:42621055-42621105	NHBE	bronchial:	n/a
29	chr3:42621055-42621105	HL-60	blood:	n/a
30	chr3:42621055-42621105	HMEC	breast:	n/a
31	chr3:42621055-42621105	LNCaP	prostate:	n/a
32	chr3:42621055-42621105	HUVEC	blood vessel:	n/a
33	chr3:42621055-42621105	BE2_C	brain:	n/a
34	chr3:42621055-42621105	H1-hESC	embryonic stem cell:	embryo
35	chr3:42621055-42621105	NHDF-neo	bronchial:	n/a
36	chr3:42621055-42621105	AG04450	lung:	fetal
37	chr3:42621055-42621105	HRE	kidney:	n/a
38	chr3:42621055-42621105	HIPEpiC	eye:	n/a
39	chr3:42621055-42621105	GM12891	blood:	n/a
40	chr3:42621055-42621105	HCT-116	colon:	n/a
41	chr3:42621055-42621105	AG09309	skin:	n/a
42	chr3:42621055-42621105	PANC-1	pancreas:	n/a
43	chr3:42621055-42621105	RPTEC	kidney:	n/a
44	chr3:42621055-42621105	GM12892	blood:	n/a
45	chr3:42621055-42621105	HPAEpiC	pulmonary alveolar:	n/a
46	chr3:42621055-42621105	HCPEpiC	choroid plexus:	n/a
47	chr3:42621055-42621105	AoSMC	blood vessel:	n/a
48	chr3:42621055-42621105	GM12878	blood:	n/a
49	chr3:42621055-42621105	T-47D	breast:	n/a
50	chr3:42621055-42621105	IMR90	lung:	fetal

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:42540384..42544045-chr3:42620631..42622853,3	K562	blood:
2	chr3:42620803..42625287-chr3:42629964..42635186,7	MCF-7	breast:
3	chr3:42620456..42625490-chr3:42691753..42697487,7	K562	blood:
4	chr3:42619900..42621497-chr3:42638395..42640003,2	MCF-7	breast:

No data

Variant related genes	Relation type
SS18L2	CpG island
ENSG00000230084	Chromatin interaction
ENSG00000114853	Chromatin interaction
ENSG00000008324	Chromatin interaction
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs13064597	0.84[EUR][1000 genomes]
rs13067987	0.97[EUR][1000 genomes]
rs13072295	0.81[EUR][1000 genomes]
rs13085143	0.80[EUR][1000 genomes]
rs13085695	0.81[EUR][1000 genomes]
rs13089845	0.81[EUR][1000 genomes]
rs13090902	0.81[EUR][1000 genomes]
rs13093680	0.81[EUR][1000 genomes]
rs13095447	0.81[EUR][1000 genomes]
rs13100261	0.83[EUR][1000 genomes]
rs17030458	0.96[EUR][1000 genomes]
rs17074662	0.81[EUR][1000 genomes]
rs17074673	0.81[EUR][1000 genomes]
rs17074674	0.81[EUR][1000 genomes]
rs17074693	0.81[EUR][1000 genomes]
rs2284303	0.81[EUR][1000 genomes]
rs2284304	0.81[EUR][1000 genomes]
rs2300057	0.81[EUR][1000 genomes]
rs2300058	0.81[EUR][1000 genomes]
rs2302352	0.81[EUR][1000 genomes]
rs33969824	0.81[EUR][1000 genomes]
rs339705	0.88[EUR][1000 genomes]
rs33984028	0.81[EUR][1000 genomes]
rs34077739	0.80[EUR][1000 genomes]
rs34196076	0.80[EUR][1000 genomes]
rs34243788	0.83[EUR][1000 genomes]
rs34683820	0.81[EUR][1000 genomes]
rs34762478	0.81[EUR][1000 genomes]
rs34801786	0.81[EUR][1000 genomes]
rs34852409	0.81[EUR][1000 genomes]
rs34977988	0.81[EUR][1000 genomes]
rs35216140	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35384559	0.83[EUR][1000 genomes]
rs35676838	0.81[EUR][1000 genomes]
rs35871059	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35890296	0.81[EUR][1000 genomes]
rs36033201	0.81[EUR][1000 genomes]
rs36043081	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3774401	0.81[EUR][1000 genomes]
rs3774402	0.81[EUR][1000 genomes]
rs3774404	0.81[EUR][1000 genomes]
rs3774407	0.81[EUR][1000 genomes]
rs3846058	0.81[EUR][1000 genomes]
rs3846059	0.81[EUR][1000 genomes]
rs3856737	0.81[EUR][1000 genomes]
rs3900780	0.97[EUR][1000 genomes]
rs55994846	0.94[EUR][1000 genomes]
rs56047094	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56797870	0.81[EUR][1000 genomes]
rs57259216	0.81[EUR][1000 genomes]
rs58645732	0.83[EUR][1000 genomes]
rs58825152	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58868911	0.81[EUR][1000 genomes]
rs59914338	0.81[EUR][1000 genomes]
rs60232916	0.81[EUR][1000 genomes]
rs60348477	0.81[EUR][1000 genomes]
rs60535002	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61149998	0.81[EUR][1000 genomes]
rs6441928	0.81[EUR][1000 genomes]
rs67059259	0.81[EUR][1000 genomes]
rs67174294	0.84[EUR][1000 genomes]
rs67583158	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6771105	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6778982	0.81[EUR][1000 genomes]
rs6782164	0.81[EUR][1000 genomes]
rs67832425	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6788548	0.81[EUR][1000 genomes]
rs6790204	0.97[EUR][1000 genomes]
rs6793186	0.81[EUR][1000 genomes]
rs6795296	0.81[EUR][1000 genomes]
rs6797491	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6797545	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs68004576	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs68028490	0.81[EUR][1000 genomes]
rs68071013	0.81[EUR][1000 genomes]
rs68190114	0.87[ASN][1000 genomes]
rs71323162	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72864022	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72864072	0.81[EUR][1000 genomes]
rs73829255	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7614219	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7616701	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7617403	0.81[EUR][1000 genomes]
rs7617736	0.81[EUR][1000 genomes]
rs7624628	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7623867	SEC22C	cis	Muscle Skeletal	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42603000-42622800	Weak transcription	Colonic Mucosa	Colon
2	chr3:42604200-42622800	Weak transcription	Psoas Muscle	Psoas
3	chr3:42604200-42623000	Weak transcription	Esophagus	oesophagus
4	chr3:42604600-42622400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:42605000-42621400	Weak transcription	HMEC	breast
6	chr3:42605200-42622400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:42607800-42621600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:42607800-42622800	Weak transcription	Pancreas	Pancrea
9	chr3:42608000-42623000	Weak transcription	Gastric	stomach
10	chr3:42608600-42621400	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:42608600-42622800	Weak transcription	Aorta	Aorta
12	chr3:42609000-42621600	Weak transcription	NHLF	lung
13	chr3:42609000-42622800	Weak transcription	HSMMtube	muscle
14	chr3:42609000-42623000	Weak transcription	Spleen	Spleen
15	chr3:42609200-42621200	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:42609200-42621600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:42609200-42621600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:42609200-42621800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:42609200-42622400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:42609600-42623000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:42610000-42622000	Weak transcription	Osteobl	bone
22	chr3:42610400-42622600	Weak transcription	Right Ventricle	heart
23	chr3:42610600-42622200	Weak transcription	NH-A	brain
24	chr3:42610600-42623000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:42611000-42621800	Weak transcription	Liver	Liver
26	chr3:42611200-42621600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:42611200-42622000	Weak transcription	Brain Substantia Nigra	brain
28	chr3:42611400-42621800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:42611400-42622800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:42611600-42621200	Weak transcription	HepG2	liver
31	chr3:42611600-42621600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:42611600-42622800	Weak transcription	Ovary	ovary
33	chr3:42611800-42621600	Weak transcription	Adipose Nuclei	Adipose
34	chr3:42611800-42621800	Weak transcription	Fetal Heart	heart
35	chr3:42614200-42621800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:42614200-42622200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:42614200-42622800	Weak transcription	Left Ventricle	heart
38	chr3:42615000-42623000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:42615000-42623000	Weak transcription	Lung	lung
40	chr3:42615200-42622600	Weak transcription	Thymus	Thymus
41	chr3:42615600-42621400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr3:42616200-42621600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:42616600-42622600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:42616600-42622600	Weak transcription	Fetal Stomach	stomach
45	chr3:42616600-42622800	Weak transcription	Placenta	Placenta
46	chr3:42616800-42622000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:42616800-42622200	Weak transcription	Fetal Intestine Large	intestine
48	chr3:42617000-42621800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr3:42617000-42622400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:42617200-42621200	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links