Variant report

Variant	rs13064954
Chromosome Location	chr3:156854742-156854743
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156394321..156397041-chr3:156854404..156856931,2	MCF-7	breast:
2	chr3:156847271..156850096-chr3:156851185..156855376,4	K562	blood:
3	chr3:156852948..156855056-chr3:156876407..156878368,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163659	Chromatin interaction
ENSG00000163660	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10440022	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs12634613	1.00[CEU][hapmap]
rs12696046	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs13060940	1.00[CEU][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13064720	0.94[YRI][hapmap]
rs13072252	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs13072425	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13076599	0.84[EUR][1000 genomes]
rs13077564	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs13078493	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs13084377	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13090731	0.84[EUR][1000 genomes]
rs13091531	1.00[CEU][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13319063	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs13319093	1.00[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13321401	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs13324111	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13325320	1.00[CEU][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs13326278	0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13326287	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs16827382	1.00[CEU][hapmap]
rs28513929	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34154019	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34300533	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35196422	0.97[EUR][1000 genomes]
rs35295311	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35988323	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3749215	0.85[JPT][hapmap]
rs66686295	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6764639	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs71310497	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9289976	0.86[CHB][hapmap]
rs9289977	0.86[CHB][hapmap]
rs9812766	1.00[CEU][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9814142	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9817693	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9821290	1.00[CEU][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs9827476	1.00[CEU][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9829650	0.84[EUR][1000 genomes]
rs9830661	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9856475	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9863805	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9866141	1.00[CEU][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9868982	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9870220	0.85[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349885	chr3:156685409-156878910	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
2	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Smoking cessation in chronic obstructive pulmonary disease	21685187	GWAS catalog
Diabetic retinopathy	21441570	GWAS catalog

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156842400-156855600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:156843000-156855600	Enhancers	Osteobl	bone
3	chr3:156845400-156855600	Enhancers	NHDF-Ad	bronchial
4	chr3:156845600-156854800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:156845600-156855600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:156846800-156855000	Weak transcription	Fetal Kidney	kidney
7	chr3:156847000-156855400	Enhancers	Fetal Heart	heart
8	chr3:156848200-156855600	Enhancers	HMEC	breast
9	chr3:156848400-156855600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:156848400-156855600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:156848400-156866000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:156848400-156866000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:156848600-156855200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:156848600-156855200	Enhancers	Fetal Muscle Leg	muscle
15	chr3:156848600-156855400	Enhancers	HSMM	muscle
16	chr3:156848600-156855600	Enhancers	Brain Cingulate Gyrus	brain
17	chr3:156848600-156855600	Enhancers	Brain Hippocampus Middle	brain
18	chr3:156848600-156855600	Enhancers	Brain Substantia Nigra	brain
19	chr3:156848600-156856400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr3:156848600-156876600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:156848800-156855400	Weak transcription	Primary B cells from cord blood	blood
22	chr3:156849000-156854800	Weak transcription	Brain Germinal Matrix	brain
23	chr3:156849000-156855600	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr3:156849000-156855800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:156849000-156860000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:156849000-156861000	Weak transcription	Dnd41	blood
27	chr3:156849000-156861800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:156849000-156862400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:156849200-156855200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:156849200-156855400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:156849200-156856000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:156849200-156861600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:156849200-156861600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:156849400-156855000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr3:156849400-156855200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:156849400-156861600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr3:156849800-156864000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr3:156850000-156855200	Weak transcription	Primary T cells from cord blood	blood
39	chr3:156850000-156855200	Enhancers	Pancreas	Pancrea
40	chr3:156850000-156855600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr3:156850000-156860200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:156850200-156854800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:156850200-156855000	Enhancers	Aorta	Aorta
44	chr3:156850200-156855000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:156850400-156860800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:156850400-156861600	Weak transcription	Hela-S3	cervix
47	chr3:156850600-156855400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr3:156850800-156855000	Enhancers	Right Ventricle	heart
49	chr3:156850800-156855200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:156851000-156861000	Weak transcription	HUVEC	blood vessel

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