Variant report

Variant	rs4689865
Chromosome Location	chr4:7801370-7801371
allele	C/G
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:1)
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	chr4:7801337-7801387	HepG2	liver:	n/a
2	chr4:7801337-7801387	RPTEC	kidney:	n/a
3	chr4:7801337-7801387	AG04450	lung:	fetal
4	chr4:7801337-7801387	HEK293	kidney:	embryo
5	chr4:7801337-7801387	HRE	kidney:	n/a
6	chr4:7801337-7801387	NHBE	bronchial:	n/a
7	chr4:7801337-7801387	ovcar-3	ovarian:	n/a
8	chr4:7801337-7801387	ECC-1	luminal epithelium:	n/a
9	chr4:7801337-7801387	GM19239	blood:	n/a
10	chr4:7801337-7801387	HRPEpiC	eye:	n/a
11	chr4:7801337-7801387	CMK	blood:	n/a
12	chr4:7801337-7801387	HPAEpiC	pulmonary alveolar:	n/a
13	chr4:7801337-7801387	SKMC	muscle:	n/a
14	chr4:7801337-7801387	HUVEC	blood vessel:	n/a
15	chr4:7801337-7801387	PFSK-1	brain:	n/a
16	chr4:7801337-7801387	HEEpiC	esophagus:	n/a
17	chr4:7801337-7801387	GM12878	blood:	n/a
18	chr4:7801337-7801387	Hela-S3	cervix:	n/a
19	chr4:7801337-7801387	SK-N-SH	brain:	n/a
20	chr4:7801337-7801387	HAEpiC	amniotic membrane:	n/a
21	chr4:7801337-7801387	MCF10A-Er-Src	breast:	n/a
22	chr4:7801337-7801387	K562	blood:	n/a
23	chr4:7801337-7801387	GM12892	blood:	n/a
24	chr4:7801337-7801387	ProgFib	skin:	n/a
25	chr4:7801337-7801387	AG10803	skin:	n/a
26	chr4:7801337-7801387	HIPEpiC	eye:	n/a
27	chr4:7801337-7801387	NT2-D1	testis:	n/a
28	chr4:7801337-7801387	AG09319	gingival:	n/a
29	chr4:7801337-7801387	SK-N-SH_RA	brain:	n/a
30	chr4:7801337-7801387	H1-hESC	embryonic stem cell:	embryo
31	chr4:7801337-7801387	NHDF-neo	bronchial:	n/a
32	chr4:7801337-7801387	T-47D	breast:	n/a
33	chr4:7801337-7801387	BJ	skin:	n/a
34	chr4:7801337-7801387	AG09309	skin:	n/a
35	chr4:7801337-7801387	GM06990	blood:	n/a
36	chr4:7801337-7801387	GM12891	blood:	n/a
37	chr4:7801337-7801387	Jurkat	blood:	n/a
38	chr4:7801337-7801387	SK-N-MC	brain:	n/a
39	chr4:7801337-7801387	IMR90	lung:	fetal
40	chr4:7801337-7801387	LNCaP	prostate:	n/a
41	chr4:7801337-7801387	NH-A	brain:	n/a
42	chr4:7801337-7801387	PANC-1	pancreas:	n/a
43	chr4:7801337-7801387	AG04449	skin:	fetal
44	chr4:7801337-7801387	HCF	heart:	n/a
45	chr4:7801337-7801387	U87	brain:	n/a
46	chr4:7801337-7801387	Hepatocyte	liver:	n/a
47	chr4:7801337-7801387	HRCEpiC	kidney:	n/a
48	chr4:7801337-7801387	HL-60	blood:	n/a
49	chr4:7801337-7801387	HNPCEpiC	eye:	n/a
50	chr4:7801337-7801387	SAEC	small airway:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7799366..7802066-chr4:7938906..7941900,2	MCF-7	breast:

No data

Variant related genes	Relation type
AFAP1	CpG island
ENSG00000196526	Chromatin interaction
ENSG00000228919	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10009045	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10018256	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10049998	0.81[JPT][hapmap]
rs11932843	0.83[JPT][hapmap]
rs13131154	0.82[JPT][hapmap]
rs13140004	0.83[JPT][hapmap]
rs17770147	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs17770177	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs2067842	1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2891927	0.83[JPT][hapmap]
rs3934540	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4234831	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4256209	0.83[JPT][hapmap]
rs4296663	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs4411970	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs4443285	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4447865	1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4487321	0.83[JPT][hapmap]
rs4579115	1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4689860	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4689875	1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4696742	0.83[JPT][hapmap]
rs4696772	0.81[JPT][hapmap]
rs6446624	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6446625	1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6446627	0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6446629	0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6814649	1.00[YRI][hapmap]
rs6824266	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs6826354	1.00[YRI][hapmap]
rs6828574	0.83[JPT][hapmap]
rs6828858	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6829537	1.00[YRI][hapmap]
rs6829710	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6832352	0.81[JPT][hapmap]
rs6833054	0.83[JPT][hapmap]
rs6834502	1.00[YRI][hapmap]
rs6839744	1.00[YRI][hapmap]
rs6845014	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs6848279	1.00[YRI][hapmap]
rs6848487	1.00[YRI][hapmap]
rs6856371	1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6856795	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71612280	0.83[EUR][1000 genomes]
rs7654361	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7682202	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs7682611	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7684718	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7697255	0.81[JPT][hapmap]
rs9683795	1.00[YRI][hapmap]
rs9996019	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1006642	chr4:7786980-7811291	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
2	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:7776400-7806800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:7781600-7807400	Weak transcription	Brain Angular Gyrus	brain
5	chr4:7783800-7806200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:7784000-7801800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:7784000-7821200	Weak transcription	Small Intestine	intestine
8	chr4:7784200-7802200	Weak transcription	Aorta	Aorta
9	chr4:7784200-7802800	Strong transcription	Fetal Muscle Trunk	muscle
10	chr4:7784800-7803400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:7785800-7803800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:7787000-7829400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr4:7789200-7806600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:7790800-7803600	Strong transcription	HSMM	muscle
15	chr4:7791000-7801400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:7791000-7806600	Weak transcription	Psoas Muscle	Psoas
17	chr4:7791000-7829400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr4:7791400-7806600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:7792200-7803200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr4:7792600-7802800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:7792600-7803400	Strong transcription	A549	lung
22	chr4:7792800-7803000	Strong transcription	HSMMtube	muscle
23	chr4:7793200-7803800	Strong transcription	NH-A	brain
24	chr4:7794400-7803600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:7794800-7803400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:7795600-7803800	Weak transcription	Fetal Kidney	kidney
27	chr4:7795800-7803800	Weak transcription	Fetal Heart	heart
28	chr4:7796000-7803400	Strong transcription	HUVEC	blood vessel
29	chr4:7796600-7803400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:7796800-7804200	Strong transcription	NHEK	skin
31	chr4:7797000-7807000	Weak transcription	Liver	Liver
32	chr4:7797200-7803000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:7797200-7803800	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr4:7797600-7802400	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr4:7797600-7802800	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr4:7797600-7803000	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr4:7797600-7803200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr4:7797600-7803200	Strong transcription	Fetal Stomach	stomach
39	chr4:7797800-7802800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:7797800-7802800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:7797800-7802800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr4:7797800-7802800	Strong transcription	Placenta	Placenta
43	chr4:7797800-7803000	Strong transcription	NHLF	lung
44	chr4:7797800-7803200	Strong transcription	NHDF-Ad	bronchial
45	chr4:7797800-7803400	Strong transcription	Fetal Intestine Large	intestine
46	chr4:7797800-7803600	Strong transcription	Fetal Muscle Leg	muscle
47	chr4:7798200-7807200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:7798400-7803000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr4:7798600-7803000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr4:7798600-7803000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links