Variant report

Variant	rs13024811
Chromosome Location	chr2:38980231-38980232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38976218..38980921-chr2:39003670..39007764,15	K562	blood:
2	chr2:38824074..38831950-chr2:38975822..38980618,12	MCF-7	breast:
3	chr2:38975148..38982473-chr2:39000165..39007764,21	K562	blood:
4	chr2:38879772..38882593-chr2:38978947..38981476,2	K562	blood:
5	chr2:38977122..38981176-chr2:38994666..38999219,6	K562	blood:
6	chr2:38824770..38827325-chr2:38977013..38980268,3	MCF-7	breast:
7	chr2:38973912..38980240-chr2:38989822..38999883,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235586	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000232114	Chromatin interaction
ENSG00000227238	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10197412	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs10865143	0.91[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.83[ASN][1000 genomes]
rs11124646	0.92[CEU][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs11898812	0.91[CHB][hapmap]
rs12472454	0.90[ASN][1000 genomes]
rs12474770	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12618118	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs12621103	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12991609	0.85[ASN][1000 genomes]
rs1529625	0.82[CHB][hapmap]
rs1979143	0.81[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap]
rs2037875	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs3097713	0.80[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs3097714	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap]
rs3099952	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3099960	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3099961	0.84[ASN][1000 genomes]
rs3099965	0.81[ASN][1000 genomes]
rs3099968	0.81[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs3099971	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3112178	1.00[CHB][hapmap]
rs3112183	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112184	0.91[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3112186	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3112188	0.91[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3112189	0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3112191	0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3112192	0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3112194	0.82[ASN][1000 genomes]
rs3112196	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs3112198	0.85[ASN][1000 genomes]
rs3112200	0.80[ASW][hapmap];0.83[LWK][hapmap]
rs3112204	0.84[ASN][1000 genomes]
rs3112209	0.81[EUR][1000 genomes]
rs3112215	0.96[CEU][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs3134628	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3134629	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3134630	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3134637	0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35387882	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731838	1.00[CHB][hapmap];0.81[GIH][hapmap]
rs4670892	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4670894	0.85[EUR][1000 genomes]
rs6715866	1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.86[ASN][1000 genomes]
rs6717670	0.91[CHB][hapmap]
rs6746818	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13024811	DHX57	cis	cerebellum	SCAN
rs13024811	SFRS7	Cis_1M	lymphoblastoid	RTeQTL
rs13024811	MORN2	cis	cerebellum	SCAN
rs13024811	GALM	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38979000-38981400	Weak transcription	Ovary	ovary
2	chr2:38979200-38980800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:38979200-38981400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:38979200-38981400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:38979200-38981400	Weak transcription	Right Atrium	heart
6	chr2:38979200-38983800	Weak transcription	HSMM	muscle
7	chr2:38979200-39005000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:38979400-38980800	Weak transcription	GM12878-XiMat	blood
9	chr2:38979400-38981000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:38979400-38981000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr2:38979400-38981000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:38979400-38981000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:38979400-38981000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:38979400-38981000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:38979400-38981000	Weak transcription	Liver	Liver
16	chr2:38979400-38981000	Weak transcription	Stomach Mucosa	stomach
17	chr2:38979400-38981000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr2:38979400-38981200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:38979400-38981200	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr2:38979400-38981200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr2:38979400-38981200	Weak transcription	Primary B cells from cord blood	blood
22	chr2:38979400-38981200	Weak transcription	Adipose Nuclei	Adipose
23	chr2:38979400-38981200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr2:38979400-38981400	Weak transcription	NHDF-Ad	bronchial
25	chr2:38979400-38981400	Weak transcription	Osteobl	bone
26	chr2:38979400-38981600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:38979600-38980800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:38979600-38981000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr2:38979600-38981000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr2:38979600-38981000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:38979600-38981000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr2:38979600-38981000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr2:38979600-38981000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:38979600-38981000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:38979600-38981000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:38979600-38981000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:38979600-38981000	Weak transcription	Fetal Intestine Small	intestine
38	chr2:38979600-38981200	Weak transcription	Primary T cells from cord blood	blood
39	chr2:38979800-38980800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:38979800-38980800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:38979800-38980800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr2:38979800-38980800	Weak transcription	HepG2	liver
43	chr2:38979800-38981000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:38979800-38981000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr2:38979800-38981000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr2:38979800-38981000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:38979800-38981200	Weak transcription	Dnd41	blood
48	chr2:38979800-38981400	Weak transcription	A549	lung

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