Variant report

Variant	rs12673746
Chromosome Location	chr7:128116352-128116353
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr7:128116271-128117196	A549	lung:	n/a	chr7:128116476-128116486
2	SIN3AK20	chr7:128116251-128117202	A549	lung:	n/a	n/a
3	MAX	chr7:128116349-128117102	K562	blood:	n/a	chr7:128116610-128116620
4	HEY1	chr7:128116288-128117446	K562	blood:	n/a	n/a
5	E2F6	chr7:128116330-128117094	K562	blood:	n/a	chr7:128116711-128116723 chr7:128116726-128116738 chr7:128116727-128116734 chr7:128116727-128116734 chr7:128116722-128116737 chr7:128116722-128116737 chr7:128116727-128116734 chr7:128116725-128116736 chr7:128116723-128116737 chr7:128116726-128116735
6	MXI1	chr7:128116227-128117779	IMR90	lung:	n/a	n/a
7	POLR2A	chr7:128116339-128117212	GM12891	blood:	n/a	n/a
8	MTA3	chr7:128116195-128117064	GM12878	blood:	n/a	n/a
9	TAF1	chr7:128116339-128117412	A549	lung:	n/a	n/a
10	MXI1	chr7:128116167-128117916	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr7:128116227-128117123	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr7:128116324-128117291	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr7:128116343-128117094	HUVEC	blood vessel:	n/a	n/a
14	ZC3H11A	chr7:128116341-128116951	K562	blood:	n/a	n/a
15	HCFC1	chr7:128116301-128117565	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr7:128116324-128117423	Hela-S3	cervix:	n/a	n/a
17	HA-E2F1	chr7:128116325-128117491	MCF-7	breast:	n/a	chr7:128116711-128116723 chr7:128116726-128116738 chr7:128116727-128116734 chr7:128116727-128116734 chr7:128116722-128116737 chr7:128116727-128116734 chr7:128116726-128116737 chr7:128116723-128116737 chr7:128116726-128116735
18	POLR2A	chr7:128116294-128117422	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr7:128116348-128117117	GM12891	blood:	n/a	n/a
20	E2F4	chr7:128116156-128116999	MCF10A-Er-Src	breast:	n/a	chr7:128116711-128116723 chr7:128116726-128116738 chr7:128116727-128116734 chr7:128116727-128116734 chr7:128116722-128116737 chr7:128116725-128116736 chr7:128116722-128116737 chr7:128116727-128116734 chr7:128116723-128116737 chr7:128116726-128116735
21	SIX5	chr7:128116136-128117234	A549	lung:	n/a	n/a
22	SP1	chr7:128116318-128117075	A549	lung:	n/a	chr7:128116757-128116767 chr7:128116757-128116767
23	POLR2A	chr7:128116287-128117409	GM12878	blood:	n/a	n/a
24	NFIC	chr7:128116219-128117339	GM12878	blood:	n/a	n/a
25	POLR2A	chr7:128116324-128117436	K562	blood:	n/a	n/a
26	POLR2A	chr7:128116243-128117446	GM12892	blood:	n/a	n/a
27	TRIM28	chr7:128116257-128117749	K562	blood:	n/a	n/a
28	TBP	chr7:128116308-128117117	K562	blood:	n/a	n/a
29	RELA	chr7:128116348-128117005	GM18505	blood:	n/a	chr7:128116655-128116664 chr7:128116655-128116664
30	CBX3	chr7:128116163-128117737	K562	blood:	n/a	n/a
31	BCL3	chr7:128116351-128117099	A549	lung:	n/a	chr7:128116670-128116678 chr7:128116654-128116663
32	POLR2A	chr7:128116328-128117762	PBDE	blood:	n/a	n/a
33	TAF1	chr7:128116312-128117512	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr7:128116346-128117378	GM12878	blood:	n/a	n/a
35	CBX3	chr7:128116351-128117049	K562	blood:	n/a	n/a
36	TEAD4	chr7:128116225-128117373	K562	blood:	n/a	chr7:128116528-128116537
37	EP300	chr7:128116349-128116993	K562	blood:	n/a	n/a
38	POLR2A	chr7:128116337-128117144	GM12891	blood:	n/a	n/a
39	STAT5A	chr7:128116266-128117479	K562	blood:	n/a	chr7:128117365-128117377
40	MYC	chr7:128116191-128117324	K562	blood:	n/a	chr7:128116610-128116620
41	POLR2A	chr7:128116203-128117204	GM12892	blood:	n/a	n/a
42	GABPA	chr7:128116309-128117467	A549	lung:	n/a	n/a
43	POLR2A	chr7:128116268-128117225	U87	brain:	n/a	n/a
44	PML	chr7:128116307-128117444	GM12878	blood:	n/a	n/a
45	POLR2A	chr7:128116348-128117108	K562	blood:	n/a	n/a
46	POLR2A	chr7:128116333-128117270	IMR90	lung:	n/a	n/a
47	POLR2A	chr7:128116246-128117442	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr7:128116287-128117344	GM12878	blood:	n/a	n/a
49	TEAD4	chr7:128116285-128117067	HepG2	liver:	n/a	chr7:128116528-128116537
50	POLR2A	chr7:128116233-128117417	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:128049014..128051472-chr7:128115731..128117859,3	K562	blood:
2	chr7:128115173..128117389-chr7:128298817..128301721,2	K562	blood:
3	chr7:128094286..128097516-chr7:128115288..128118444,4	K562	blood:
4	chr7:128116092..128118343-chr7:128171049..128172892,4	K562	blood:
5	chr7:128095923..128097516-chr7:128115288..128116864,2	K562	blood:
6	chr14:35008396..35009205-chr7:128116073..128116780,2	Hela-S3	cervix:

Variant related genes	Relation type
METTL2B	TF binding region
ENSG00000240758	Chromatin interaction
ENSG00000242588	Chromatin interaction
ENSG00000106348	Chromatin interaction
ENSG00000273184	Chromatin interaction
ENSG00000129518	Chromatin interaction
ENSG00000135245	Chromatin interaction
ENSG00000271529	Chromatin interaction
ENSG00000273270	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10954186	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11973151	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11978885	0.91[ASN][1000 genomes]
rs12670251	0.88[EUR][1000 genomes]
rs12671449	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12671633	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34648097	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56174902	0.83[ASN][1000 genomes]
rs56329212	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62481136	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62481142	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62481155	0.92[EUR][1000 genomes]
rs62483264	0.92[EUR][1000 genomes]
rs62483275	0.91[EUR][1000 genomes]
rs62483280	0.88[EUR][1000 genomes]
rs62483350	0.81[EUR][1000 genomes]
rs7799914	0.89[EUR][1000 genomes]
rs7809300	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831124	chr7:127970345-128147910	Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv966883	chr7:128107081-128142581	Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12673746	RP11-274B21.4	cis	Whole Blood	GTEx
rs12673746	RP11-274B21.2	cis	Adipose Subcutaneous	GTEx
rs12673746	RP11-274B21.4	cis	Adipose Subcutaneous	GTEx
rs12673746	RP11-274B21.1	cis	lung	GTEx
rs12673746	RP11-274B21.1	cis	Adipose Subcutaneous	GTEx
rs12673746	ENSG00000165055	cis	multi-tissue	Pritchard

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128096400-128116400	Weak transcription	Lung	lung
2	chr7:128097800-128116400	Weak transcription	Fetal Stomach	stomach
3	chr7:128097800-128116400	Weak transcription	Gastric	stomach
4	chr7:128097800-128116400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:128098200-128116400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:128098200-128116400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:128099000-128116400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:128099200-128116400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr7:128099400-128116400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:128099800-128116400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr7:128099800-128116400	Weak transcription	Fetal Intestine Small	intestine
12	chr7:128099800-128116400	Weak transcription	Ovary	ovary
13	chr7:128100000-128116400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:128100000-128116400	Weak transcription	Brain Hippocampus Middle	brain
15	chr7:128100000-128116400	Weak transcription	Esophagus	oesophagus
16	chr7:128100000-128116400	Weak transcription	Fetal Brain Male	brain
17	chr7:128103800-128116400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr7:128104600-128116400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr7:128104600-128116400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:128108200-128116400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:128108600-128116400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr7:128109000-128116400	Weak transcription	Fetal Muscle Leg	muscle
23	chr7:128114800-128116400	Weak transcription	Placenta	Placenta
24	chr7:128114800-128116400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr7:128115800-128116400	Weak transcription	Right Atrium	heart
26	chr7:128116200-128116400	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr7:128116200-128116400	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr7:128116200-128116400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr7:128116200-128116400	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr7:128116200-128116400	Enhancers	Primary B cells from cord blood	blood
31	chr7:128116200-128116400	Enhancers	Primary B cells from peripheral blood	blood
32	chr7:128116200-128116400	Enhancers	Primary T cells from cord blood	blood
33	chr7:128116200-128116400	Active TSS	Primary hematopoietic stem cells	blood
34	chr7:128116200-128116400	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr7:128116200-128116400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr7:128116200-128116400	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr7:128116200-128116400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr7:128116200-128116400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr7:128116200-128116400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr7:128116200-128116400	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr7:128116200-128116400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr7:128116200-128116400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr7:128116200-128116400	Enhancers	Brain Cingulate Gyrus	brain
44	chr7:128116200-128116400	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr7:128116200-128116400	Enhancers	Colon Smooth Muscle	Colon
46	chr7:128116200-128116400	Enhancers	Fetal Heart	heart
47	chr7:128116200-128116400	Enhancers	Fetal Kidney	kidney
48	chr7:128116200-128116400	Enhancers	Fetal Lung	lung
49	chr7:128116200-128116400	Enhancers	Rectal Smooth Muscle	rectum
50	chr7:128116200-128116400	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links