Variant report

Variant	rs9917245
Chromosome Location	chr2:10541712-10541713
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10538831..10544260-chr2:10544573..10548851,6	K562	blood:
2	chr2:10539200..10541759-chr2:10543040..10545009,3	K562	blood:
3	chr2:10533744..10537127-chr2:10539374..10542865,3	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11676661	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11688771	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2270302	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3771124	0.85[ASN][1000 genomes]
rs3771125	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3771127	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3771130	0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs3771139	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56044909	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7580561	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs7582990	0.80[CHB][hapmap]
rs7594864	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530829	chr2:10357105-10655131	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv873641	chr2:10480415-10544640	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv873643	chr2:10535481-10583160	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv873644	chr2:10537347-10576424	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv873645	chr2:10537347-10612091	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
6	esv3439050	chr2:10539751-10542249	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1007185	chr2:10540386-10791743	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9917245	HPCAL1	cis	multi-tissue	Pritchard
rs9917245	RNF144A	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10527200-10542400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr2:10530600-10544400	Weak transcription	Brain Angular Gyrus	brain
3	chr2:10531000-10542400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:10531000-10544600	Weak transcription	NHLF	lung
5	chr2:10531200-10542400	Weak transcription	HSMMtube	muscle
6	chr2:10531200-10542400	Weak transcription	NH-A	brain
7	chr2:10531200-10544200	Weak transcription	Brain Substantia Nigra	brain
8	chr2:10533000-10551800	Weak transcription	Ovary	ovary
9	chr2:10533400-10549200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:10533600-10544200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:10533600-10544200	Weak transcription	Fetal Brain Female	brain
12	chr2:10534000-10545400	Weak transcription	Fetal Lung	lung
13	chr2:10537000-10543000	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr2:10537000-10543400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:10537400-10542600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:10537400-10542600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr2:10537400-10542800	Enhancers	Left Ventricle	heart
18	chr2:10537600-10542600	Genic enhancers	Lung	lung
19	chr2:10538200-10541800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:10538200-10542800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:10538200-10544400	Weak transcription	Psoas Muscle	Psoas
22	chr2:10539000-10542000	Strong transcription	Thymus	Thymus
23	chr2:10539400-10544800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:10539600-10542000	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr2:10539600-10542800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:10539600-10544400	Weak transcription	Fetal Kidney	kidney
27	chr2:10539800-10542000	Enhancers	Right Atrium	heart
28	chr2:10539800-10542200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:10539800-10542600	Genic enhancers	Gastric	stomach
30	chr2:10539800-10542800	Enhancers	Stomach Mucosa	stomach
31	chr2:10540000-10542000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr2:10540000-10542600	Genic enhancers	Primary B cells from cord blood	blood
33	chr2:10540000-10542600	Enhancers	Right Ventricle	heart
34	chr2:10540200-10542000	Enhancers	Primary hematopoietic stem cells	blood
35	chr2:10540200-10542600	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr2:10540200-10543000	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr2:10540200-10544800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:10540400-10542000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr2:10540600-10541800	Enhancers	Fetal Thymus	thymus
40	chr2:10540600-10542000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr2:10540600-10542000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:10540600-10542000	Enhancers	Esophagus	oesophagus
43	chr2:10540600-10542600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:10540600-10542600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:10540600-10542600	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr2:10540600-10542600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr2:10540600-10542800	Enhancers	Primary T cells fromperipheralblood	blood
48	chr2:10540600-10542800	Enhancers	Small Intestine	intestine
49	chr2:10540600-10543000	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr2:10540800-10541800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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