Variant report

Variant	rs12117465
Chromosome Location	chr1:113942043-113942044
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113941512..113944463-chr1:113944848..113948985,5	K562	blood:
2	chr1:113934960..113937525-chr1:113941030..113943620,2	K562	blood:
3	chr1:113930487..113934541-chr1:113941004..113944111,4	K562	blood:
4	chr1:113934736..113938053-chr1:113941345..113946073,4	K562	blood:
5	chr1:113930552..113936083-chr1:113941902..113950756,10	MCF-7	breast:
6	chr1:113932799..113934589-chr1:113941238..113945556,5	K562	blood:

Variant related genes	Relation type
ENSG00000081026	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11102629	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11102646	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs11578447	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs11579386	0.87[CEU][hapmap]
rs12117919	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12119281	0.96[EUR][1000 genomes]
rs12125741	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12127683	0.96[EUR][1000 genomes]
rs12130729	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12130763	0.96[EUR][1000 genomes]
rs12131115	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes]
rs12134802	0.94[EUR][1000 genomes]
rs12135714	0.94[EUR][1000 genomes]
rs12144505	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12145834	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17031640	0.87[CEU][hapmap]
rs17031645	0.87[CEU][hapmap]
rs17031648	0.87[CEU][hapmap]
rs17448063	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17461007	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17461231	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes]
rs17507884	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs1936931	0.96[EUR][1000 genomes]
rs2359415	0.96[EUR][1000 genomes]
rs55710846	0.93[EUR][1000 genomes]
rs6537788	1.00[CEU][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6671518	0.87[CEU][hapmap]
rs6696459	0.87[CEU][hapmap]
rs7514186	0.87[CEU][hapmap]
rs7528311	0.87[CEU][hapmap]
rs7533429	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes]
rs7555259	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv999873	chr1:113840351-113949453	Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	nsv1010110	chr1:113856612-113969417	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
4	nsv1014757	chr1:113861524-113969417	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113934800-113945200	Weak transcription	Gastric	stomach
2	chr1:113934800-113945200	Weak transcription	Left Ventricle	heart
3	chr1:113935200-113943200	Weak transcription	HUVEC	blood vessel
4	chr1:113935200-113945400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:113935200-113949400	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:113935600-113949400	Weak transcription	Aorta	Aorta
7	chr1:113936000-113945200	Weak transcription	Right Atrium	heart
8	chr1:113936000-113952400	Weak transcription	Fetal Stomach	stomach
9	chr1:113936800-113945200	Weak transcription	Brain Germinal Matrix	brain
10	chr1:113936800-113945200	Weak transcription	Pancreas	Pancrea
11	chr1:113937200-113948200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:113937600-113945600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:113937600-113947200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:113937600-113963400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:113937800-113946400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:113938000-113946200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:113939600-113947800	Weak transcription	HepG2	liver
18	chr1:113939800-113942200	Enhancers	A549	lung
19	chr1:113939800-113943400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:113939800-113944000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:113939800-113947200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:113939800-113947200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:113939800-113953400	Weak transcription	NHDF-Ad	bronchial
24	chr1:113940000-113943400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:113940200-113945600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:113940200-113948000	Weak transcription	Liver	Liver
27	chr1:113940200-113952200	Weak transcription	HMEC	breast
28	chr1:113940200-113987000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:113940800-113943200	Weak transcription	Stomach Mucosa	stomach
30	chr1:113940800-113945400	Weak transcription	Fetal Brain Female	brain
31	chr1:113940800-113950000	Weak transcription	Fetal Intestine Large	intestine
32	chr1:113940800-113952200	Weak transcription	Hela-S3	cervix
33	chr1:113941400-113942200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:113941400-113942200	Enhancers	Fetal Lung	lung
35	chr1:113941600-113943400	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr1:113941800-113942200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr1:113941800-113942200	Enhancers	Fetal Intestine Small	intestine
38	chr1:113941800-113942200	Enhancers	Ovary	ovary
39	chr1:113941800-113952200	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:113942000-113947200	Weak transcription	Fetal Heart	heart

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