Variant report

Variant	rs6808742
Chromosome Location	chr3:47051512-47051513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:87)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:87 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr3:47050770-47052797	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:47050603-47051909	GM18526	blood:	n/a	n/a
3	CTCF	chr3:47051420-47051570	GM12870	blood:	n/a	n/a
4	YY1	chr3:47050806-47051587	GM12891	blood:	n/a	n/a
5	RAD21	chr3:47051485-47051645	H1-hESC	embryonic stem cell:	n/a	chr3:47051582-47051595
6	CTCF	chr3:47051400-47051550	HRE	kidney:	n/a	n/a
7	POLR2A	chr3:47050449-47052087	H1-hESC	embryonic stem cell:	n/a	n/a
8	RUNX3	chr3:47050867-47051663	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:47050724-47052790	GM12878	blood:	n/a	n/a
10	CTCF	chr3:47051420-47051570	GM12866	blood:	n/a	n/a
11	TBP	chr3:47050694-47051680	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:47051378-47051591	HCT-116	colon:	n/a	n/a
13	CTCF	chr3:47051440-47051590	HRPEpiC	eye:	n/a	n/a
14	CTCF	chr3:47051340-47051630	GM12866	blood:	n/a	chr3:47051394-47051407
15	CTCF	chr3:47051507-47051578	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr3:47051417-47051597	GM19239	blood:	n/a	n/a
17	MAX	chr3:47050386-47051780	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr3:47050631-47052806	GM12891	blood:	n/a	n/a
19	CTCF	chr3:47051460-47051610	HBMEC	blood vessel:	n/a	n/a
20	POLR2A	chr3:47050884-47051679	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr3:47051480-47051630	HRE	kidney:	n/a	n/a
22	MXI1	chr3:47051366-47051565	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr3:47050917-47053219	K562	blood:	n/a	n/a
24	POLR2A	chr3:47050649-47052230	GM12878	blood:	n/a	n/a
25	CTCF	chr3:47051480-47051630	GM06990	blood:	n/a	n/a
26	CTCF	chr3:47051400-47051550	GM12871	blood:	n/a	n/a
27	POLR2A	chr3:47050455-47052000	GM19193	blood:	n/a	n/a
28	CTCF	chr3:47051400-47051550	HA-sp	spinal cord:	n/a	n/a
29	CTCF	chr3:47051420-47051570	SAEC	small airway:	n/a	n/a
30	TEAD4	chr3:47051237-47051686	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr3:47051436-47051567	GM12878	blood:	n/a	n/a
32	RUNX3	chr3:47050808-47051785	GM12878	blood:	n/a	n/a
33	ELF1	chr3:47050683-47051981	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:47051130-47053407	K562	blood:	n/a	n/a
35	POU2F2	chr3:47050626-47051691	GM12878	blood:	n/a	chr3:47051615-47051627
36	TAF7	chr3:47050665-47051519	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr3:47050610-47053359	GM12892	blood:	n/a	n/a
38	POLR2A	chr3:47050904-47052240	GM12891	blood:	n/a	n/a
39	POLR2A	chr3:47050873-47051588	GM12878	blood:	n/a	n/a
40	ZNF143	chr3:47051454-47051540	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr3:47050965-47051578	K562	blood:	n/a	n/a
42	POLR2A	chr3:47050818-47052522	GM12891	blood:	n/a	n/a
43	CTCF	chr3:47051500-47051650	HRPEpiC	eye:	n/a	n/a
44	STAT5A	chr3:47051008-47051674	GM12878	blood:	n/a	n/a
45	CTCF	chr3:47051480-47051630	HPF	lung:	n/a	n/a
46	TAF1	chr3:47050824-47051665	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr3:47051480-47051630	BJ	skin:	n/a	n/a
48	POLR2A	chr3:47050701-47052139	GM18505	blood:	n/a	n/a
49	SIN3A	chr3:47050835-47051657	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr3:47050662-47051675	HUVEC	blood vessel:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:47020574..47023054-chr3:47051075..47053218,2	MCF-7	breast:
2	chr3:47047312..47050228-chr3:47050509..47055807,4	MCF-7	breast:
3	chr17:41464193..41465701-chr3:47050147..47051667,2	K562	blood:
4	chr3:47038738..47041744-chr3:47049789..47052323,3	MCF-7	breast:
5	chr11:62607697..62610640-chr3:47050167..47053167,3	K562	blood:
6	chr3:47051147..47052167-chr3:73160089..73160623,3	Hela-S3	cervix:
7	chr3:47051147..47052167-chr3:73159942..73160626,4	HCT-116	colon:

No data

Variant related genes	Relation type
NRADDP	TF binding region
ENSG00000223247	Chromatin interaction
ENSG00000160799	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000160796	Chromatin interaction
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10433549	0.84[EUR][1000 genomes]
rs10461018	0.88[EUR][1000 genomes]
rs1079276	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1108301	0.91[EUR][1000 genomes]
rs11130110	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11130111	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130112	0.91[EUR][1000 genomes]
rs11716553	0.86[EUR][1000 genomes]
rs11720139	0.85[EUR][1000 genomes]
rs11917474	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12152493	0.90[EUR][1000 genomes]
rs12491473	0.88[EUR][1000 genomes]
rs12630534	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13062681	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13066214	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13077398	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13087426	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13091054	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1463393	0.88[EUR][1000 genomes]
rs17784127	0.84[EUR][1000 genomes]
rs1869869	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1869871	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2061197	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2278963	0.86[EUR][1000 genomes]
rs2305634	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305635	0.86[EUR][1000 genomes]
rs2305638	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385867	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34103310	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34344887	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4078466	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4082155	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4234465	0.91[EUR][1000 genomes]
rs4682831	0.91[EUR][1000 genomes]
rs4682837	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4682844	0.87[EUR][1000 genomes]
rs55724164	0.82[EUR][1000 genomes]
rs55843455	0.90[EUR][1000 genomes]
rs55927279	0.81[EUR][1000 genomes]
rs56217494	0.84[EUR][1000 genomes]
rs56249396	0.81[EUR][1000 genomes]
rs61729713	0.91[EUR][1000 genomes]
rs62246375	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62246398	0.82[EUR][1000 genomes]
rs62248439	0.88[EUR][1000 genomes]
rs66539935	0.91[EUR][1000 genomes]
rs66564457	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6763236	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6767218	0.81[EUR][1000 genomes]
rs6774733	0.88[EUR][1000 genomes]
rs6785790	0.82[AFR][1000 genomes]
rs6794193	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs749511	0.86[EUR][1000 genomes]
rs7610636	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7617689	0.88[EUR][1000 genomes]
rs7621911	0.82[ASN][1000 genomes]
rs7625067	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7625070	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7628747	0.88[EUR][1000 genomes]
rs7633698	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7636252	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7637302	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7640397	0.80[AFR][1000 genomes];0.88[EUR][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	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS 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	25 gene(s)	inside rSNPs	diseases
2	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv876757	chr3:47018214-47058057	Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6808742	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs6808742	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47031000-47053000	Strong transcription	Dnd41	blood
2	chr3:47039800-47058000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr3:47042200-47053000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:47043800-47057800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:47045000-47057600	Weak transcription	HepG2	liver
6	chr3:47048600-47055800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:47049000-47055000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:47049000-47055400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:47049800-47051600	Genic enhancers	Primary monocytes fromperipheralblood	blood
10	chr3:47049800-47058200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:47050000-47052000	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr3:47050200-47051600	Active TSS	H1 Cell Line	embryonic stem cell
13	chr3:47050200-47051600	Active TSS	Brain Angular Gyrus	brain
14	chr3:47050200-47051800	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr3:47050200-47052000	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr3:47050200-47052200	Enhancers	Fetal Brain Male	brain
17	chr3:47050200-47058200	Weak transcription	Hela-S3	cervix
18	chr3:47050200-47059000	Weak transcription	A549	lung
19	chr3:47050200-47063800	Weak transcription	Stomach Mucosa	stomach
20	chr3:47050400-47051600	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr3:47050400-47051600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:47050400-47051600	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr3:47050400-47051600	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr3:47050400-47051600	Active TSS	Duodenum Mucosa	Duodenum
25	chr3:47050400-47051600	Active TSS	Fetal Kidney	kidney
26	chr3:47050400-47051600	Active TSS	Psoas Muscle	Psoas
27	chr3:47050400-47051600	Active TSS	Rectal Smooth Muscle	rectum
28	chr3:47050400-47051800	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr3:47050400-47051800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:47050400-47051800	Active TSS	Brain Anterior Caudate	brain
31	chr3:47050400-47051800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr3:47050400-47052000	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:47050400-47052200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:47050400-47057600	Weak transcription	K562	blood
35	chr3:47050600-47051600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:47050600-47051600	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr3:47050600-47051600	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr3:47050600-47051600	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr3:47050600-47051600	Active TSS	Aorta	Aorta
40	chr3:47050600-47051600	Active TSS	Brain Cingulate Gyrus	brain
41	chr3:47050600-47051600	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr3:47050600-47051600	Active TSS	Brain Substantia Nigra	brain
43	chr3:47050600-47051600	Active TSS	Fetal Intestine Large	intestine
44	chr3:47050600-47051600	Active TSS	Fetal Lung	lung
45	chr3:47050600-47051600	Active TSS	Left Ventricle	heart
46	chr3:47050600-47051600	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr3:47050600-47051800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr3:47050600-47051800	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr3:47050600-47052000	Active TSS	H9 Cell Line	embryonic stem cell
50	chr3:47050600-47052000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links