Variant report

Variant	rs7770443
Chromosome Location	chr6:34246714-34246715
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:34246480-34247005	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:34246504-34247453	K562	blood:	n/a	n/a
3	POLR2A	chr6:34244327-34250971	K562	blood:	n/a	n/a
4	POLR2A	chr6:34246547-34246817	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr6:34246662-34247314	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:34246568-34247365	K562	blood:	n/a	n/a
7	POLR2A	chr6:34246558-34246866	GM12891	blood:	n/a	n/a
8	POLR2A	chr6:34246703-34246719	MCF-7	breast:	n/a	n/a
9	POLR2A	chr6:34246466-34246841	K562	blood:	n/a	n/a
10	POLR2A	chr6:34246483-34246805	K562	blood:	n/a	n/a
11	POLR2A	chr6:34246206-34246853	K562	blood:	n/a	n/a
12	POLR2A	chr6:34246646-34247260	HL-60	blood:	n/a	n/a
13	POLR2A	chr6:34246429-34246755	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr6:34245487-34246922	HL-60	blood:	n/a	n/a
15	POLR2A	chr6:34246633-34247140	A549	lung:	n/a	n/a
16	POLR2A	chr6:34246630-34246721	GM12878	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:34211942..34216855-chr6:34244859..34247946,7	K562	blood:
2	chr6:34214507..34216888-chr6:34245546..34249056,4	K562	blood:
3	chr6:34202426..34206348-chr6:34246132..34251181,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000225339	TF binding region
ENSG00000186577	Chromatin interaction
ENSG00000137309	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10484267	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs10484268	1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs1057691	1.00[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs1060308	1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs10648	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1127084	0.84[EUR][1000 genomes]
rs1265	1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs12654	0.84[EUR][1000 genomes]
rs13466	1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs16883137	1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs16883475	1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs16883896	1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs16888452	0.84[EUR][1000 genomes]
rs16889678	0.80[ASW][hapmap];0.93[YRI][hapmap]
rs17628798	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs17628946	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs17629180	1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs17629270	1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs17696583	1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs17696774	1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs17696829	1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1994923	0.84[EUR][1000 genomes]
rs206922	0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs3798554	0.80[EUR][1000 genomes]
rs3798557	0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs3913009	0.85[CEU][hapmap]
rs41269032	0.83[EUR][1000 genomes]
rs41269034	0.84[EUR][1000 genomes]
rs41269036	0.84[EUR][1000 genomes]
rs41269038	0.83[EUR][1000 genomes]
rs55674397	0.84[EUR][1000 genomes]
rs55684754	0.84[EUR][1000 genomes]
rs55694290	0.83[EUR][1000 genomes]
rs55763242	0.84[EUR][1000 genomes]
rs55779010	0.84[EUR][1000 genomes]
rs55798596	0.83[EUR][1000 genomes]
rs55812200	0.84[EUR][1000 genomes]
rs55833185	0.84[EUR][1000 genomes]
rs55863933	0.84[EUR][1000 genomes]
rs55864834	0.82[EUR][1000 genomes]
rs56033036	0.84[EUR][1000 genomes]
rs56039915	0.84[EUR][1000 genomes]
rs56107559	0.84[EUR][1000 genomes]
rs56188036	0.84[EUR][1000 genomes]
rs56274913	0.84[EUR][1000 genomes]
rs56309550	0.84[EUR][1000 genomes]
rs56323997	0.84[EUR][1000 genomes]
rs56330729	0.84[EUR][1000 genomes]
rs62399870	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6911272	0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs7738665	0.83[EUR][1000 genomes]
rs7760373	0.84[EUR][1000 genomes]
rs875274	1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885781	chr6:34110257-34247661	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv462903	chr6:34110257-34263743	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv602863	chr6:34110257-34263743	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv885784	chr6:34187206-34246714	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	esv1798756	chr6:34203406-34319041	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	esv1798835	chr6:34204183-34319041	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	esv1792088	chr6:34204285-34318837	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	esv1793127	chr6:34204285-34319041	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	esv3377596	chr6:34243274-34247372	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7770443	NUDT3	cis	lymphoblastoid	seeQTL
rs7770443	NUDT3	Cis_1M	lymphoblastoid	RTeQTL
rs7770443	NUDT3	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34218200-34255000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr6:34228600-34247000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:34229000-34246800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:34233000-34251800	Weak transcription	NHDF-Ad	bronchial
5	chr6:34234200-34247600	Weak transcription	Brain Germinal Matrix	brain
6	chr6:34238400-34259400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:34239000-34247600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:34239600-34247000	Weak transcription	Fetal Brain Female	brain
9	chr6:34240200-34249000	Weak transcription	NHLF	lung
10	chr6:34240200-34250200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:34240200-34255200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:34240400-34249600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:34240400-34251800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:34240400-34255000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:34240400-34259800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:34240400-34259800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr6:34240600-34247200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr6:34240600-34250400	Weak transcription	Brain Substantia Nigra	brain
19	chr6:34240600-34269200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:34240800-34261000	Weak transcription	Fetal Kidney	kidney
21	chr6:34241000-34248600	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr6:34241400-34260000	Weak transcription	Esophagus	oesophagus
23	chr6:34241600-34249600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:34241600-34250400	Weak transcription	Fetal Thymus	thymus
25	chr6:34241600-34252800	Weak transcription	Stomach Mucosa	stomach
26	chr6:34241800-34247800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:34242000-34247000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:34242000-34252800	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:34242200-34249600	Weak transcription	HUVEC	blood vessel
30	chr6:34242200-34250200	Weak transcription	GM12878-XiMat	blood
31	chr6:34243200-34248400	Enhancers	Psoas Muscle	Psoas
32	chr6:34243400-34247400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr6:34243600-34246800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr6:34243600-34250800	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr6:34243600-34252600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:34243600-34257200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr6:34243800-34247000	Weak transcription	Primary B cells from cord blood	blood
38	chr6:34244000-34248200	Weak transcription	HSMM	muscle
39	chr6:34244200-34251800	Weak transcription	Brain Anterior Caudate	brain
40	chr6:34244200-34260000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr6:34244400-34256600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr6:34244400-34273400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr6:34244800-34249000	Weak transcription	Fetal Lung	lung
44	chr6:34244800-34251400	Weak transcription	Osteobl	bone
45	chr6:34244800-34251600	Weak transcription	NHEK	skin
46	chr6:34245000-34246800	Weak transcription	Fetal Heart	heart
47	chr6:34245000-34246800	Weak transcription	Thymus	Thymus
48	chr6:34245000-34250000	Weak transcription	Placenta	Placenta
49	chr6:34245000-34250600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:34245000-34259800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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