Variant report

Variant	rs4598779
Chromosome Location	chr13:40235373-40235374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:40235362..40236092-chr14:53549695..53550409,2	MCF-7	breast:
2	chr13:40229027..40231888-chr13:40233465..40236904,4	MCF-7	breast:
3	chr13:40228867..40231362-chr13:40235168..40238124,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133103	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10162010	0.94[ASN][1000 genomes]
rs10467367	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs10467368	0.94[ASN][1000 genomes]
rs4129745	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4132636	1.00[ASN][1000 genomes]
rs4132637	1.00[ASN][1000 genomes]
rs4254189	0.91[ASN][1000 genomes]
rs4261404	1.00[ASN][1000 genomes]
rs4275735	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4277227	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4294679	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs4300508	0.97[ASN][1000 genomes]
rs4306389	0.83[ASN][1000 genomes]
rs4321067	1.00[ASN][1000 genomes]
rs4334152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4363738	1.00[ASN][1000 genomes]
rs4368051	1.00[ASN][1000 genomes]
rs4432137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4457870	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4485233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4492929	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4514547	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4551909	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4556673	1.00[ASN][1000 genomes]
rs4566029	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4569133	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4586300	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4606581	0.93[ASN][1000 genomes]
rs4636783	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941940	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943688	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943689	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943692	1.00[ASN][1000 genomes]
rs4943693	0.96[ASN][1000 genomes]
rs6563737	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563738	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6563739	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6563740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7320424	1.00[ASN][1000 genomes]
rs7324826	1.00[ASN][1000 genomes]
rs7325354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7326555	1.00[ASN][1000 genomes]
rs7326699	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs7327674	1.00[ASN][1000 genomes]
rs7330016	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7330515	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74044148	0.94[ASN][1000 genomes]
rs7991151	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7991758	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7993726	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7993729	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7994665	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7998582	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7999758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9315723	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9315724	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9532416	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9532417	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548872	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548873	0.91[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548877	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548878	1.00[ASN][1000 genomes]
rs9548881	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548883	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs9548884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548885	1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs9548895	1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs9566469	1.00[ASN][1000 genomes]
rs9594362	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9603589	0.93[ASN][1000 genomes]
rs9603591	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9603592	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9603593	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs9603594	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs9603597	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs9603602	1.00[CHB][hapmap];0.87[JPT][hapmap];0.96[ASN][1000 genomes]
rs9603603	0.82[GIH][hapmap]
rs9943	0.84[GIH][hapmap];0.85[TSI][hapmap]

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	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv832586	chr13:40222880-40379063	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv870429	chr13:40235061-40265634	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4598779	COG6	cis	multi-tissue	Pritchard
rs4598779	COG6	cis	Muscle Skeletal	GTEx
rs4598779	EXOSC8	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40230600-40252200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:40230600-40254600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:40230600-40254600	Weak transcription	Lung	lung
4	chr13:40230600-40254800	Weak transcription	Aorta	Aorta
5	chr13:40230600-40263800	Weak transcription	Spleen	Spleen
6	chr13:40230800-40235400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr13:40230800-40236000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr13:40230800-40236200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr13:40230800-40236200	Weak transcription	Fetal Intestine Small	intestine
10	chr13:40230800-40238800	Weak transcription	Fetal Kidney	kidney
11	chr13:40230800-40238800	Weak transcription	HSMM	muscle
12	chr13:40230800-40239400	Weak transcription	HSMMtube	muscle
13	chr13:40230800-40239600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr13:40230800-40239800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr13:40230800-40240000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr13:40230800-40246600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr13:40230800-40254600	Weak transcription	Left Ventricle	heart
18	chr13:40230800-40254600	Weak transcription	Psoas Muscle	Psoas
19	chr13:40230800-40254800	Weak transcription	Fetal Thymus	thymus
20	chr13:40230800-40256400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr13:40230800-40258400	Weak transcription	Colonic Mucosa	Colon
22	chr13:40230800-40262000	Weak transcription	Thymus	Thymus
23	chr13:40230800-40275000	Weak transcription	Right Ventricle	heart
24	chr13:40231000-40235400	Weak transcription	Primary B cells from cord blood	blood
25	chr13:40231000-40237800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr13:40231000-40238800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr13:40231000-40239200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr13:40231000-40241600	Weak transcription	Hela-S3	cervix
29	chr13:40231000-40243800	Weak transcription	Fetal Heart	heart
30	chr13:40231000-40252200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr13:40231000-40252800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr13:40231000-40254400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr13:40231000-40254400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr13:40231000-40254600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr13:40231000-40254600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr13:40231000-40254600	Weak transcription	NHLF	lung
37	chr13:40231000-40256400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr13:40231000-40256400	Weak transcription	NHEK	skin
39	chr13:40231000-40257200	Weak transcription	HMEC	breast
40	chr13:40231000-40261800	Weak transcription	Brain Substantia Nigra	brain
41	chr13:40231000-40266200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr13:40231000-40270800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr13:40231000-40286000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr13:40231200-40236200	Weak transcription	K562	blood
45	chr13:40231200-40239600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr13:40231200-40254400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr13:40231200-40254600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr13:40231200-40254800	Weak transcription	Fetal Stomach	stomach
49	chr13:40231400-40237800	Weak transcription	Fetal Muscle Leg	muscle
50	chr13:40231400-40253600	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links