Variant report

Variant	rs17038524
Chromosome Location	chr2:33522178-33522179
allele	G/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	chr2:33521965-33522472	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:33515586..33518253-chr2:33521124..33522863,2	MCF-7	breast:
2	chr2:33521500..33523864-chr2:33524061..33525573,2	K562	blood:
3	chr2:33514241..33517210-chr2:33520355..33523749,3	K562	blood:
4	chr2:33513308..33515964-chr2:33519124..33522873,3	K562	blood:

Variant related genes	Relation type
LTBP1	TF binding region
ENSG00000049323	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11674005	0.87[EUR][1000 genomes]
rs11682866	1.00[CEU][hapmap]
rs11685019	0.87[EUR][1000 genomes]
rs11689160	1.00[CEU][hapmap]
rs11689377	1.00[CEU][hapmap]
rs11694122	1.00[CEU][hapmap]
rs11694765	1.00[CEU][hapmap]
rs17012718	0.91[YRI][hapmap]
rs17012763	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17012773	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17012805	0.95[YRI][hapmap]
rs55873210	0.87[EUR][1000 genomes]
rs56203414	0.82[EUR][1000 genomes]
rs57189309	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61151459	0.81[AFR][1000 genomes]
rs6708335	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6730165	0.85[YRI][hapmap]
rs73925006	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	nsv873791	chr2:33489975-33586776	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv1011020	chr2:33508811-33527784	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33492400-33547400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:33501200-33528800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:33502600-33537000	Weak transcription	Fetal Intestine Large	intestine
4	chr2:33505000-33526200	Weak transcription	Placenta	Placenta
5	chr2:33507000-33528600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:33517000-33522800	Weak transcription	K562	blood
7	chr2:33517000-33524600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:33517000-33525400	Weak transcription	Right Ventricle	heart
9	chr2:33517000-33526600	Weak transcription	Fetal Stomach	stomach
10	chr2:33517000-33528800	Weak transcription	Psoas Muscle	Psoas
11	chr2:33517000-33529200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:33517000-33529400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:33517000-33529600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:33517200-33522200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:33517200-33522800	Weak transcription	HSMMtube	muscle
16	chr2:33517200-33525800	Weak transcription	Liver	Liver
17	chr2:33517200-33533000	Weak transcription	Brain Substantia Nigra	brain
18	chr2:33517200-33533200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:33517200-33537400	Weak transcription	Fetal Brain Male	brain
20	chr2:33517200-33545000	Weak transcription	Fetal Kidney	kidney
21	chr2:33517200-33545800	Weak transcription	Fetal Lung	lung
22	chr2:33517200-33546400	Weak transcription	Brain Angular Gyrus	brain
23	chr2:33517600-33532600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:33517600-33532800	Weak transcription	Brain Anterior Caudate	brain
25	chr2:33517800-33543400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:33518400-33522800	Weak transcription	NHDF-Ad	bronchial
27	chr2:33520400-33522200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:33520800-33522200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:33520800-33522200	Genic enhancers	Fetal Heart	heart
30	chr2:33520800-33522400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:33520800-33523400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr2:33521000-33523400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:33521000-33523600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr2:33521400-33522800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr2:33521400-33523600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr2:33521400-33525400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:33521600-33522800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:33521600-33522800	Weak transcription	Osteobl	bone
39	chr2:33521600-33523400	Enhancers	Ovary	ovary
40	chr2:33521800-33522200	Weak transcription	NHLF	lung
41	chr2:33521800-33522600	Enhancers	HUVEC	blood vessel
42	chr2:33521800-33525800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:33522000-33522200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:33522000-33522200	Enhancers	Left Ventricle	heart
45	chr2:33522000-33522200	Genic enhancers	Stomach Smooth Muscle	stomach
46	chr2:33522000-33522400	Enhancers	Fetal Muscle Leg	muscle
47	chr2:33522000-33522400	Genic enhancers	NH-A	brain
48	chr2:33522000-33522800	Enhancers	Aorta	Aorta
49	chr2:33522000-33523000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:33522000-33523400	Enhancers	Adipose Nuclei	Adipose

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