Variant report

Variant	rs6690619
Chromosome Location	chr1:153765399-153765400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153763846..153765824-chr1:153774129..153777112,2	MCF-7	breast:
2	chr1:153764439..153766738-chr1:153770528..153772998,3	K562	blood:
3	chr1:153762961..153765422-chr1:153766931..153769360,3	K562	blood:
4	chr1:153764458..153766239-chr1:153894173..153897068,2	K562	blood:
5	chr1:153747124..153749409-chr1:153765103..153767331,2	MCF-7	breast:
6	chr1:153765340..153768610-chr1:153963132..153965319,3	K562	blood:
7	chr1:153764949..153767946-chr1:153918589..153920254,2	MCF-7	breast:
8	chr1:153758281..153760333-chr1:153763925..153766016,2	K562	blood:
9	chr1:153756292..153758003-chr1:153762929..153766093,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000207039	Chromatin interaction
ENSG00000231827	Chromatin interaction
ENSG00000143614	Chromatin interaction
ENSG00000198837	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000177954	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10127484	1.00[JPT][hapmap]
rs10908578	1.00[JPT][hapmap]
rs11264573	1.00[JPT][hapmap]
rs11264736	1.00[JPT][hapmap];0.96[YRI][hapmap]
rs1127091	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1139620	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12117078	1.00[JPT][hapmap]
rs12120118	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12124424	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12130611	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12133492	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12133923	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12142733	1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs12738361	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17364880	1.00[JPT][hapmap]
rs2252508	1.00[JPT][hapmap];0.96[YRI][hapmap]
rs4276953	0.80[EUR][1000 genomes]
rs4341393	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4370789	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4451582	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4540690	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4581307	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4596938	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61803655	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6427300	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6427306	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6661009	1.00[JPT][hapmap]
rs6664419	0.84[EUR][1000 genomes]
rs6668066	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6677794	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6700115	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs72694233	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7414227	1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs7415004	0.83[AFR][1000 genomes]
rs7522030	1.00[JPT][hapmap]
rs7532974	0.90[AFR][1000 genomes]
rs7532982	0.85[AFR][1000 genomes]
rs7541871	0.87[ASN][1000 genomes]
rs7554469	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9426935	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9426938	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9427220	0.84[EUR][1000 genomes]
rs9427232	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9427233	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][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	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
4	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv464039	chr1:153708906-153801098	Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv547941	chr1:153708906-153801098	Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
9	nsv515962	chr1:153752139-153773429	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153756600-153767000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:153757000-153779200	Weak transcription	Dnd41	blood
3	chr1:153761800-153765400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:153762400-153776600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:153762600-153777600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr1:153762600-153777600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:153762600-153779600	Weak transcription	Gastric	stomach
8	chr1:153762600-153779600	Weak transcription	Pancreas	Pancrea
9	chr1:153762800-153766000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:153762800-153766600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:153763000-153765800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:153763000-153767600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:153763400-153772000	Weak transcription	Lung	lung
14	chr1:153763600-153765400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr1:153763600-153765400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:153763600-153765600	Enhancers	GM12878-XiMat	blood
17	chr1:153763600-153765800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr1:153763600-153771600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:153763600-153772000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:153763600-153776800	Weak transcription	Right Atrium	heart
21	chr1:153763600-153777800	Weak transcription	Fetal Intestine Large	intestine
22	chr1:153763600-153780000	Weak transcription	Aorta	Aorta
23	chr1:153763600-153780000	Weak transcription	Ovary	ovary
24	chr1:153763600-153780800	Weak transcription	Colonic Mucosa	Colon
25	chr1:153763800-153767400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:153763800-153773200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:153763800-153779400	Weak transcription	Brain Substantia Nigra	brain
28	chr1:153764000-153766000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:153764000-153768400	Weak transcription	Primary T cells from cord blood	blood
30	chr1:153764000-153777000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:153764000-153777800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:153764000-153779600	Weak transcription	Brain Angular Gyrus	brain
33	chr1:153764200-153765400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:153764200-153765400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:153764200-153765600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:153764400-153765400	Bivalent Enhancer	HepG2	liver
37	chr1:153764400-153766600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:153764400-153766600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:153764400-153767000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr1:153764400-153767200	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:153764400-153768000	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr1:153764400-153768000	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr1:153764400-153768000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr1:153764400-153768800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:153764400-153768800	Weak transcription	Liver	Liver
46	chr1:153764400-153769000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:153764400-153769600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr1:153764400-153772200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:153764400-153774000	Weak transcription	Osteobl	bone
50	chr1:153764400-153776000	Weak transcription	HSMMtube	muscle

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