Variant report

Variant	rs912646
Chromosome Location	chr1:157992292-157992293
allele	C/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	CTCF	chr1:157992174-157992293	NHEK	skin:	n/a	n/a
2	CTCF	chr1:157992240-157992390	HCM	heart:	n/a	n/a
3	CTCF	chr1:157992220-157992370	AG09319	gingival:	n/a	n/a
4	CTCF	chr1:157992160-157992310	AoAF	blood vessel:	n/a	n/a
5	CTCF	chr1:157992200-157992350	HMF	breast:	n/a	n/a
6	CTCF	chr1:157992180-157992330	AoAF	blood vessel:	n/a	n/a
7	CTCF	chr1:157992240-157992390	HCPEpiC	choroid plexus:	n/a	n/a
8	CEBPB	chr1:157992225-157992763	A549	lung:	n/a	chr1:157992503-157992516 chr1:157992503-157992516 chr1:157992505-157992516 chr1:157992503-157992514 chr1:157992503-157992516
9	CTCF	chr1:157992280-157992430	NHDF-neo	bronchial:	n/a	n/a
10	CTCF	chr1:157992180-157992330	AG09319	gingival:	n/a	n/a
11	CTCF	chr1:157992240-157992390	HVMF	connective:	n/a	n/a
12	CTCF	chr1:157992160-157992310	HMF	breast:	n/a	n/a

Variant related genes	Relation type
KIRREL-IT1	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11264876	0.83[EUR][1000 genomes]
rs17418566	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17452391	0.88[EUR][1000 genomes]
rs17453287	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1925037	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6671484	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7519243	1.00[YRI][hapmap]
rs912645	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs912647	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs927700	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823720	chr1:157978556-158034017	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:157975400-157996800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:157983800-157993200	Enhancers	Fetal Kidney	kidney
3	chr1:157984400-157995400	Weak transcription	Fetal Brain Female	brain
4	chr1:157985200-157993200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:157985200-157995000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:157985200-158006000	Weak transcription	Fetal Thymus	thymus
7	chr1:157985400-157993400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:157986000-157993000	Enhancers	Placenta Amnion	Placenta Amnion
9	chr1:157986000-157993200	Enhancers	Placenta	Placenta
10	chr1:157986200-157993200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:157986400-157993000	Enhancers	Ovary	ovary
12	chr1:157986400-157993200	Enhancers	Fetal Lung	lung
13	chr1:157986400-157993200	Enhancers	Fetal Muscle Leg	muscle
14	chr1:157987000-157993200	Enhancers	Fetal Stomach	stomach
15	chr1:157987200-157996400	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr1:157987600-157993000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr1:157987800-157993000	Enhancers	Colon Smooth Muscle	Colon
18	chr1:157987800-157993600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:157988000-157993400	Enhancers	Rectal Smooth Muscle	rectum
20	chr1:157988200-157993400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr1:157988400-157992400	Weak transcription	Esophagus	oesophagus
22	chr1:157988400-157993600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:157989000-157992600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:157989400-157992600	Weak transcription	Psoas Muscle	Psoas
25	chr1:157989400-157992600	Weak transcription	Right Ventricle	heart
26	chr1:157989400-158007400	Weak transcription	Gastric	stomach
27	chr1:157989600-157993400	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr1:157989800-157992600	Enhancers	Adipose Nuclei	Adipose
29	chr1:157989800-157993200	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr1:157989800-157993400	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr1:157989800-157993400	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr1:157989800-157993800	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr1:157990000-157992600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:157990000-157992800	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr1:157990000-157993000	Enhancers	Stomach Smooth Muscle	stomach
36	chr1:157990000-157993200	Enhancers	HUVEC	blood vessel
37	chr1:157990000-157993800	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr1:157990000-157994600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr1:157990000-157996400	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr1:157990200-157992400	Weak transcription	Lung	lung
41	chr1:157990200-157992600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:157990200-157992600	Enhancers	NHLF	lung
43	chr1:157990200-157993000	Enhancers	NH-A	brain
44	chr1:157990400-157992800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:157990800-157992600	Enhancers	H9 Cell Line	embryonic stem cell
46	chr1:157990800-157992600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:157990800-157993000	Enhancers	HSMMtube	muscle
48	chr1:157990800-157993400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:157991000-157992400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:157991000-157992400	Flanking Active TSS	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links