Variant report

Variant	rs3856058
Chromosome Location	chr1:180644569-180644570
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180600246..180602406-chr1:180641858..180644833,2	K562	blood:

Variant related genes	Relation type
ENSG00000143324	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10914061	0.90[ASN][1000 genomes]
rs10914096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12085097	0.86[EUR][1000 genomes]
rs12118646	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1339768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1970404	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2331626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2331886	1.00[CEU][hapmap];0.82[YRI][hapmap];0.94[EUR][1000 genomes]
rs2944259	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs2944262	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs3002113	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs3002114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3002115	0.88[EUR][1000 genomes]
rs3002116	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs3002117	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3002123	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3013633	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3013634	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3789366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3843278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3845406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3897798	0.92[ASN][1000 genomes]
rs4083591	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4108558	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4651073	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs66520411	0.88[EUR][1000 genomes]
rs6659049	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6659368	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6661105	0.91[CHB][hapmap]
rs6682974	0.87[EUR][1000 genomes]
rs67780680	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs72707408	0.84[EUR][1000 genomes]
rs72723045	0.88[EUR][1000 genomes]
rs7514404	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7524547	0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7541650	0.90[CHB][hapmap];0.92[ASN][1000 genomes]
rs7548318	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs7550031	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs9425881	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9970145	0.91[CHB][hapmap]
rs9970363	0.82[CHB][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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv947336	chr1:180642298-180656857	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180602000-180645200	Weak transcription	Gastric	stomach
2	chr1:180632200-180644800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:180633200-180672000	Weak transcription	K562	blood
4	chr1:180635000-180644800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:180635200-180654800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:180636400-180647200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:180636400-180651800	Weak transcription	Ovary	ovary
8	chr1:180640200-180662200	Weak transcription	Fetal Heart	heart
9	chr1:180640600-180660600	Weak transcription	Right Ventricle	heart
10	chr1:180641000-180653200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:180641200-180647400	Weak transcription	Fetal Intestine Small	intestine
12	chr1:180641200-180653400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:180641200-180662800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:180641400-180644800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:180641600-180661200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:180641800-180644800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:180642200-180658200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:180642400-180644600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:180642800-180644800	Weak transcription	Aorta	Aorta
20	chr1:180642800-180644800	Weak transcription	Small Intestine	intestine
21	chr1:180642800-180646200	Weak transcription	Pancreas	Pancrea
22	chr1:180643000-180651400	Weak transcription	Primary B cells from cord blood	blood
23	chr1:180643000-180659000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:180643200-180647200	Weak transcription	Primary T cells from cord blood	blood
25	chr1:180643800-180645000	Enhancers	H1 Cell Line	embryonic stem cell
26	chr1:180643800-180645000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:180643800-180645200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr1:180643800-180645200	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr1:180644000-180645800	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr1:180644000-180646200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:180644000-180660400	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:180644000-180660800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:180644000-180662600	Weak transcription	Left Ventricle	heart
34	chr1:180644000-180663800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:180644200-180645000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:180644200-180645400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr1:180644200-180645800	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr1:180644200-180645800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:180644400-180644600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:180644400-180644800	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr1:180644400-180644800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:180644400-180645000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:180644400-180645000	Enhancers	Stomach Mucosa	stomach
44	chr1:180644400-180645200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr1:180644400-180645200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:180644400-180645200	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr1:180644400-180645200	Enhancers	A549	lung

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