Variant report

Variant	rs7598922
Chromosome Location	chr2:39082344-39082345
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38977106..38980095-chr2:39079432..39082390,2	K562	blood:
2	chr2:39075448..39080892-chr2:39081993..39084972,5	K562	blood:
3	chr2:39082200..39083996-chr2:39090256..39092735,2	MCF-7	breast:
4	chr2:39079613..39082361-chr2:39103056..39104740,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000188010	Chromatin interaction
ENSG00000163214	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1010858	0.91[AFR][1000 genomes]
rs1010859	0.81[GIH][hapmap]
rs10173118	0.92[JPT][hapmap]
rs10173240	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10176932	0.81[JPT][hapmap]
rs10779923	0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.87[YRI][hapmap]
rs11124651	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11675110	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12373604	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12465365	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12623330	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12712621	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs12712625	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs12712626	0.92[CEU][hapmap];0.92[GIH][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12712627	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12712628	0.91[AFR][1000 genomes]
rs13029388	0.96[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13029406	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs13383541	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs1530852	1.00[JPT][hapmap]
rs1530853	1.00[JPT][hapmap]
rs17494315	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1901289	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1979142	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs3099940	0.82[CHB][hapmap]
rs3099941	0.84[GIH][hapmap]
rs3099942	0.84[GIH][hapmap]
rs3099945	0.85[CHD][hapmap];0.81[GIH][hapmap]
rs3099995	0.84[EUR][1000 genomes]
rs3100000	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs3112159	0.86[GIH][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs3112163	0.85[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs373300	0.86[ASW][hapmap];0.86[JPT][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs3770681	1.00[JPT][hapmap]
rs390008	0.81[AMR][1000 genomes]
rs3923144	0.81[GIH][hapmap]
rs4133043	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4265996	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4641916	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4670266	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4670267	0.84[CEU][hapmap];0.83[CHB][hapmap];0.87[YRI][hapmap]
rs4670899	0.81[ASW][hapmap];0.82[CEU][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.93[LWK][hapmap];0.83[MKK][hapmap]
rs6706091	0.81[ASW][hapmap];0.88[LWK][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs6710418	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6732083	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6734584	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6738403	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6741088	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6744514	0.81[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7419616	1.00[JPT][hapmap]
rs7565111	0.85[JPT][hapmap]
rs7586929	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7589162	0.81[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs9808136	1.00[YRI][hapmap];0.90[AFR][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	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7598922	ITGB1	trans	parietal	SCAN
rs7598922	DHX57	cis	cerebellum	SCAN
rs7598922	MFN1	trans	parietal	SCAN
rs7598922	SOS1	cis	lymphoblastoid	seeQTL
rs7598922	DHX57	Cis_1M	lymphoblastoid	RTeQTL
rs7598922	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	chr2:39062400-39083400	Weak transcription	NHEK	skin
14	chr2:39063600-39088400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr2:39067200-39090200	Weak transcription	Stomach Mucosa	stomach
16	chr2:39068400-39090600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:39072200-39095400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr2:39072400-39089200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:39072600-39090800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:39073000-39091200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:39073600-39090200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr2:39075200-39090800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:39076000-39090600	Strong transcription	Brain Germinal Matrix	brain
24	chr2:39076200-39090600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:39076400-39090800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:39076600-39090800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr2:39078000-39090800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:39078200-39091200	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr2:39078400-39082400	Strong transcription	Dnd41	blood
30	chr2:39078400-39090600	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr2:39078800-39084000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:39078800-39090600	Strong transcription	Osteobl	bone
33	chr2:39079200-39086000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:39079200-39086200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:39079400-39090800	Strong transcription	Primary B cells from peripheral blood	blood
36	chr2:39079600-39083000	Strong transcription	Primary hematopoietic stem cells	blood
37	chr2:39079600-39086200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:39079600-39090400	Strong transcription	Fetal Thymus	thymus
39	chr2:39079600-39090800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr2:39079600-39090800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:39079600-39090800	Strong transcription	Fetal Brain Female	brain
42	chr2:39079800-39082400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr2:39079800-39082400	Strong transcription	Fetal Lung	lung
44	chr2:39079800-39082600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:39079800-39082800	Strong transcription	Placenta	Placenta
46	chr2:39079800-39083200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr2:39079800-39083200	Strong transcription	Brain Substantia Nigra	brain
48	chr2:39079800-39084000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:39079800-39084000	Strong transcription	Brain Angular Gyrus	brain
50	chr2:39079800-39084200	Strong transcription	Ovary	ovary

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