Variant report

Variant	rs3112163
Chromosome Location	chr2:39084757-39084758
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	chr2:38976661..38978798-chr2:39083252..39086476,5	MCF-7	breast:
2	chr2:39075448..39080892-chr2:39081993..39084972,5	K562	blood:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000163214	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1010859	1.00[ASW][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.96[LWK][hapmap];0.84[MKK][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10779923	0.84[GIH][hapmap]
rs10865143	1.00[JPT][hapmap]
rs11124651	0.90[EUR][1000 genomes]
rs11681583	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11689954	0.90[CHB][hapmap]
rs11898812	1.00[JPT][hapmap]
rs12373604	0.92[EUR][1000 genomes]
rs12465365	0.80[EUR][1000 genomes]
rs12712625	0.89[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap]
rs12712626	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs12712627	0.89[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs13029388	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs13035182	0.86[AFR][1000 genomes]
rs1530852	0.81[CEU][hapmap]
rs17422748	0.87[AFR][1000 genomes]
rs1901289	0.89[GIH][hapmap]
rs1979143	0.83[ASW][hapmap];1.00[JPT][hapmap]
rs2373469	0.87[AFR][1000 genomes]
rs2373471	0.87[AFR][1000 genomes]
rs3097713	0.88[JPT][hapmap]
rs3097714	0.88[JPT][hapmap]
rs3099946	0.84[AFR][1000 genomes]
rs3099955	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3099956	0.90[CHB][hapmap]
rs3099958	0.90[CHB][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes]
rs3099968	0.83[ASW][hapmap];1.00[JPT][hapmap]
rs3099990	1.00[JPT][hapmap]
rs3099995	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3100000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3112159	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3112166	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3112175	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3112178	0.88[JPT][hapmap]
rs3112184	1.00[JPT][hapmap]
rs3112188	1.00[JPT][hapmap]
rs3112189	1.00[JPT][hapmap]
rs3112191	1.00[JPT][hapmap]
rs3112192	1.00[JPT][hapmap]
rs3112196	1.00[JPT][hapmap]
rs3134637	1.00[JPT][hapmap]
rs3923144	0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap]
rs4641916	0.86[EUR][1000 genomes]
rs4670266	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4670268	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs4670899	0.80[GIH][hapmap]
rs4670900	0.93[AFR][1000 genomes]
rs61736780	0.88[AFR][1000 genomes]
rs6710418	0.96[EUR][1000 genomes]
rs6717670	1.00[JPT][hapmap]
rs6734584	0.97[EUR][1000 genomes]
rs6736353	0.87[AFR][1000 genomes]
rs6738069	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.86[ASN][1000 genomes]
rs6738403	0.90[EUR][1000 genomes]
rs6741088	0.85[EUR][1000 genomes]
rs72797376	0.89[AFR][1000 genomes]
rs72797386	0.88[AFR][1000 genomes]
rs72797392	0.87[AFR][1000 genomes]
rs72797402	0.87[AFR][1000 genomes]
rs7565111	0.90[CHB][hapmap]
rs7598922	0.85[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs8179664	0.81[CHB][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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv2692	chr2:39065768-39111871	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3112163	DHX57	cis	cerebellum	SCAN
rs3112163	DHX57	cis	multi-tissue	Pritchard
rs3112163	DHX57	Cis_1M	lymphoblastoid	RTeQTL
rs3112163	MORN2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:39030600-39088200	Weak transcription	Fetal Heart	heart
3	chr2:39038800-39095600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:39038800-39102200	Weak transcription	Gastric	stomach
5	chr2:39039000-39085400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:39039000-39090000	Weak transcription	Esophagus	oesophagus
7	chr2:39039000-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
9	chr2:39050400-39088000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:39055200-39085600	Weak transcription	Psoas Muscle	Psoas
11	chr2:39057000-39086200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:39058000-39087800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:39063600-39088400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:39067200-39090200	Weak transcription	Stomach Mucosa	stomach
15	chr2:39068400-39090600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:39072200-39095400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:39072400-39089200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:39072600-39090800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:39073000-39091200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:39073600-39090200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:39075200-39090800	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:39076000-39090600	Strong transcription	Brain Germinal Matrix	brain
23	chr2:39076200-39090600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:39076400-39090800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:39076600-39090800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:39078000-39090800	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr2:39078200-39091200	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:39078400-39090600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr2:39078800-39090600	Strong transcription	Osteobl	bone
30	chr2:39079200-39086000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:39079200-39086200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:39079400-39090800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr2:39079600-39086200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:39079600-39090400	Strong transcription	Fetal Thymus	thymus
35	chr2:39079600-39090800	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr2:39079600-39090800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:39079600-39090800	Strong transcription	Fetal Brain Female	brain
38	chr2:39079800-39085800	Strong transcription	Thymus	Thymus
39	chr2:39079800-39086600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr2:39079800-39086600	Strong transcription	Liver	Liver
41	chr2:39079800-39089600	Strong transcription	Fetal Stomach	stomach
42	chr2:39079800-39090600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:39079800-39090600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:39079800-39090600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:39079800-39090600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:39079800-39090600	Strong transcription	Brain Anterior Caudate	brain
47	chr2:39079800-39090600	Strong transcription	Fetal Muscle Leg	muscle
48	chr2:39079800-39090600	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:39079800-39090800	Strong transcription	Adipose Nuclei	Adipose
50	chr2:39079800-39091000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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