Variant report

Variant	rs17008541
Chromosome Location	chr2:73210411-73210412
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	POLR2A	chr2:73210408-73210442	K562	blood:	n/a	n/a

Variant related genes	Relation type
SFXN5	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1046183	0.89[JPT][hapmap]
rs10496188	1.00[CEU][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13404068	0.90[CEU][hapmap];0.84[JPT][hapmap]
rs17008565	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17008579	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17008608	1.00[CEU][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2421099	0.90[CEU][hapmap];0.90[JPT][hapmap]
rs3849393	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58731407	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59108557	0.82[EUR][1000 genomes]
rs61164794	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61652727	0.82[EUR][1000 genomes]
rs62147718	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62147722	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62147726	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62147727	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62147728	0.95[EUR][1000 genomes]
rs62147731	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62147733	0.98[EUR][1000 genomes]
rs62147735	0.95[EUR][1000 genomes]
rs62147756	0.81[EUR][1000 genomes]
rs62148129	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62148130	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66570372	0.94[EUR][1000 genomes]
rs6710911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6753054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6753133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6753301	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67673165	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv532723	chr2:73088191-73219259	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv874266	chr2:73137991-73220138	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73168800-73226800	Weak transcription	NHLF	lung
2	chr2:73169200-73210600	Weak transcription	Pancreas	Pancrea
3	chr2:73176600-73227400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:73177400-73215200	Weak transcription	Osteobl	bone
5	chr2:73178000-73214800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:73181800-73215200	Weak transcription	Thymus	Thymus
7	chr2:73182800-73213000	Weak transcription	Fetal Lung	lung
8	chr2:73183200-73228200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:73185000-73214400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:73188800-73211600	Weak transcription	Primary T cells from cord blood	blood
11	chr2:73190600-73234400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:73193600-73221200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:73194200-73248800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:73194400-73211400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:73194600-73210600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:73198600-73220000	Weak transcription	Small Intestine	intestine
17	chr2:73201800-73210800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:73203200-73218400	Weak transcription	Brain Germinal Matrix	brain
19	chr2:73203400-73211200	Weak transcription	Fetal Brain Male	brain
20	chr2:73207200-73211200	Enhancers	Fetal Heart	heart
21	chr2:73207200-73213600	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr2:73207200-73214200	Enhancers	Left Ventricle	heart
23	chr2:73207800-73211000	Weak transcription	Brain Angular Gyrus	brain
24	chr2:73207800-73263200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:73208000-73215000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:73208000-73215200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:73208000-73247600	Weak transcription	Primary B cells from cord blood	blood
28	chr2:73208200-73212800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:73208200-73217000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:73208200-73218000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr2:73208200-73227000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr2:73208400-73217200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:73208400-73227400	Weak transcription	A549	lung
34	chr2:73208400-73227600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr2:73208600-73210600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:73208600-73217200	Weak transcription	NHEK	skin
37	chr2:73208600-73217800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr2:73208600-73227200	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:73209000-73210600	Weak transcription	Stomach Mucosa	stomach
40	chr2:73209000-73227000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:73209000-73227200	Weak transcription	HSMM	muscle
42	chr2:73209400-73212000	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:73209400-73218800	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr2:73209400-73219200	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr2:73209600-73211000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:73209600-73211000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr2:73209600-73211200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:73209600-73212000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:73209600-73212400	Strong transcription	Lung	lung
50	chr2:73209600-73214000	Enhancers	Right Atrium	heart

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