Variant report

Variant	rs1267673
Chromosome Location	chr7:140397792-140397793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr7:140396191-140397937	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:140395412-140398733	K562	blood:	n/a	n/a
3	REST	chr7:140395884-140397806	H1-neurons	neurons:	n/a	chr7:140397037-140397057 chr7:140397040-140397053
4	POLR2A	chr7:140396312-140398555	A549	lung:	n/a	n/a
5	MTA3	chr7:140396110-140397792	GM12878	blood:	n/a	n/a
6	POLR2A	chr7:140395870-140398317	K562	blood:	n/a	n/a
7	MAZ	chr7:140396193-140397798	IMR90	lung:	n/a	chr7:140397111-140397120 chr7:140397003-140397013 chr7:140397110-140397121 chr7:140397111-140397120 chr7:140397109-140397122
8	POLR2A	chr7:140395754-140398083	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr7:140396303-140398104	HepG2	liver:	n/a	n/a
10	SIN3AK20	chr7:140396180-140397801	SK-N-SH	brain:	n/a	n/a
11	SREBP1	chr7:140395610-140398289	GM12878	blood:	n/a	n/a
12	MXI1	chr7:140395202-140397951	SK-N-SH	brain:	n/a	chr7:140397110-140397119
13	CREB1	chr7:140396226-140397845	K562	blood:	n/a	n/a
14	POLR2A	chr7:140397567-140398143	K562	blood:	n/a	n/a
15	POLR2A	chr7:140395804-140397938	GM12878	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:140395805..140398704-chr7:140623265..140626329,4	K562	blood:
2	chr7:140175625..140180151-chr7:140394567..140398370,5	MCF-7	breast:
3	chr7:140370275..140375389-chr7:140393210..140401279,16	MCF-7	breast:
4	chr7:140394719..140399884-chr7:140712014..140716961,9	K562	blood:
5	chr7:140395267..140398426-chr7:140622802..140626309,6	K562	blood:
6	chr7:140372637..140375611-chr7:140394231..140397834,5	K562	blood:
7	chr7:140394556..140398514-chr7:140712637..140716961,7	K562	blood:
8	chr7:140394845..140398499-chr7:140712009..140715919,6	MCF-7	breast:
9	chr7:140378195..140380507-chr7:140394973..140398117,3	K562	blood:
10	chr7:140176812..140180644-chr7:140393947..140398398,4	K562	blood:
11	chr7:140371560..140374067-chr7:140396511..140398663,2	K562	blood:
12	chr7:140395386..140400852-chr7:140710628..140716984,11	MCF-7	breast:
13	chr7:140370608..140383131-chr7:140387718..140398587,28	MCF-7	breast:
14	chr7:140388053..140392866-chr7:140393585..140398020,10	MCF-7	breast:

No data

Variant related genes	Relation type
NDUFB2	TF binding region
NDUFB2-AS1	TF binding region
ENSG00000133606	Chromatin interaction
ENSG00000146966	Chromatin interaction
ENSG00000133597	Chromatin interaction
ENSG00000157764	Chromatin interaction
ENSG00000090263	Chromatin interaction
ENSG00000090266	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10232557	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10234502	0.88[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs10272940	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs10281173	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs10281508	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs10282499	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1267602	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1267603	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1267610	0.82[AFR][1000 genomes]
rs1267612	0.94[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs1267615	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1267616	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs1267618	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1267621	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1267622	0.87[ASW][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.82[AFR][1000 genomes]
rs1267623	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1267624	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1267625	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1267632	0.94[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1267634	0.94[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1267635	0.94[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1267637	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1267646	0.94[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1267647	0.94[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1267648	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs2109742	0.94[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs2109743	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs2364399	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs2535946	0.94[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs269238	0.92[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs2706774	0.94[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs2706775	0.94[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs3789806	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4140846	1.00[CHB][hapmap]
rs6464037	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs6947950	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs6954652	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs6964724	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs6966197	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs7791924	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs7792984	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs7798324	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs7801086	1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs7803738	0.87[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831157	chr7:140241339-140426876	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv3351231	chr7:140390303-140588539	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv831158	chr7:140392222-140602315	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1267673	BRAF	Cis_1M	lymphoblastoid	RTeQTL
rs1267673	ADCK2	cis	cerebellum	SCAN
rs1267673	CASP2	cis	parietal	SCAN
rs1267673	TMEM178B	cis	Esophagus Mucosa	GTEx
rs1267673	TMEM139	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140395800-140397800	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr7:140395800-140398000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr7:140396000-140397800	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr7:140396000-140398000	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr7:140396000-140398000	Active TSS	Fetal Kidney	kidney
6	chr7:140396000-140398000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr7:140396000-140398200	Active TSS	HSMMtube	muscle
8	chr7:140396200-140397800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:140396200-140397800	Active TSS	A549	lung
10	chr7:140396200-140398000	Active TSS	H9 Cell Line	embryonic stem cell
11	chr7:140396200-140398000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr7:140396200-140398000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
13	chr7:140396200-140398200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:140396400-140397800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr7:140396400-140398000	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr7:140396400-140398200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:140396600-140398200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
18	chr7:140397000-140397800	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr7:140397000-140398400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr7:140397200-140397800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr7:140397200-140397800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr7:140397200-140397800	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr7:140397200-140397800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr7:140397200-140397800	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr7:140397200-140397800	Flanking Active TSS	Fetal Muscle Trunk	muscle
26	chr7:140397200-140397800	Flanking Active TSS	Placenta	Placenta
27	chr7:140397200-140398000	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr7:140397200-140398000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr7:140397200-140398000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr7:140397200-140398000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:140397200-140398000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr7:140397200-140398000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr7:140397200-140398000	Flanking Active TSS	Liver	Liver
34	chr7:140397200-140398000	Flanking Active TSS	Fetal Heart	heart
35	chr7:140397200-140398000	Flanking Active TSS	Fetal Muscle Leg	muscle
36	chr7:140397200-140398200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:140397200-140398200	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr7:140397200-140398200	Flanking Active TSS	Fetal Thymus	thymus
39	chr7:140397200-140398200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr7:140397200-140398200	Flanking Active TSS	Osteobl	bone
41	chr7:140397200-140398400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr7:140397400-140397800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr7:140397400-140397800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr7:140397400-140397800	Flanking Active TSS	Esophagus	oesophagus
45	chr7:140397400-140397800	Flanking Active TSS	Fetal Brain Male	brain
46	chr7:140397400-140397800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
47	chr7:140397400-140397800	Flanking Active TSS	Thymus	Thymus
48	chr7:140397400-140398000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr7:140397400-140398000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr7:140397400-140398000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links