Variant report

Variant	rs4670899
Chromosome Location	chr2:39105781-39105782
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:39102312..39104681-chr2:39105607..39108211,2	K562	blood:
2	chr2:39052271..39054519-chr2:39105359..39107014,2	K562	blood:

Variant related genes	Relation type
ENSG00000188010	Chromatin interaction
ENSG00000163214	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1010858	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1010859	0.84[CEU][hapmap];0.89[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs10181808	0.80[EUR][1000 genomes]
rs10204999	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10779923	0.89[CHB][hapmap];0.87[GIH][hapmap]
rs11124654	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1131752	0.80[EUR][1000 genomes]
rs11689954	0.92[CEU][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12621073	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12623330	0.81[CEU][hapmap];0.91[YRI][hapmap]
rs12712621	0.81[JPT][hapmap]
rs12712625	0.81[ASW][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap]
rs12712626	0.83[GIH][hapmap]
rs12712627	0.81[ASW][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap]
rs12712628	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13029388	0.82[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs13035182	0.87[EUR][1000 genomes]
rs17422748	0.88[EUR][1000 genomes]
rs1901289	0.88[CHB][hapmap];0.92[GIH][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap]
rs2060743	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2060744	0.84[AFR][1000 genomes]
rs2373473	0.82[CHB][hapmap]
rs3099940	0.82[EUR][1000 genomes]
rs3099941	0.80[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.83[EUR][1000 genomes]
rs3099942	0.81[CHB][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs3099943	0.82[CHB][hapmap]
rs3099945	0.82[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap]
rs3099951	0.85[AFR][1000 genomes]
rs3099958	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs3099959	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[EUR][1000 genomes]
rs3099998	0.81[EUR][1000 genomes]
rs3112163	0.80[GIH][hapmap]
rs373300	0.92[CEU][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs389023	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3923144	0.88[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes]
rs4265996	0.83[CHB][hapmap]
rs4670267	0.83[CHB][hapmap]
rs4670268	0.83[EUR][1000 genomes]
rs6544180	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6706091	0.92[CEU][hapmap];0.88[CHB][hapmap];0.85[LWK][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6706186	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6738069	0.83[GIH][hapmap];0.82[EUR][1000 genomes]
rs6738403	0.81[ASN][1000 genomes]
rs6741088	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6744514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754902	0.85[EUR][1000 genomes]
rs7598922	0.81[ASW][hapmap];0.82[CEU][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.93[LWK][hapmap];0.83[MKK][hapmap]
rs9808136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4670899	DHX57	Cis_1M	lymphoblastoid	RTeQTL
rs4670899	MORN2	cis	parietal	SCAN
rs4670899	ITGB1	trans	parietal	SCAN
rs4670899	DHX57	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39103800-39107800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr2:39103800-39107800	Weak transcription	Placenta	Placenta
3	chr2:39103800-39113400	Weak transcription	Pancreas	Pancrea
4	chr2:39103800-39113400	Weak transcription	HSMMtube	muscle
5	chr2:39103800-39114000	Weak transcription	Lung	lung
6	chr2:39103800-39120200	Weak transcription	Left Ventricle	heart
7	chr2:39104000-39105800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr2:39104000-39107600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:39104000-39111200	Weak transcription	HUVEC	blood vessel
10	chr2:39104000-39112600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:39104000-39112600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:39104000-39113200	Weak transcription	Right Ventricle	heart
13	chr2:39104000-39113400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:39104000-39114200	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr2:39104200-39107000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:39104200-39107400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:39104200-39107600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:39104200-39107600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:39104200-39107600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:39104200-39107600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:39104200-39107600	Weak transcription	Liver	Liver
22	chr2:39104200-39107600	Weak transcription	Brain Anterior Caudate	brain
23	chr2:39104200-39107600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:39104200-39108000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr2:39104200-39108000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:39104200-39108000	Weak transcription	Hela-S3	cervix
27	chr2:39104200-39108200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:39104200-39108600	Weak transcription	Dnd41	blood
29	chr2:39104200-39109000	Weak transcription	Stomach Mucosa	stomach
30	chr2:39104200-39109600	Weak transcription	Adipose Nuclei	Adipose
31	chr2:39104200-39110000	Weak transcription	HMEC	breast
32	chr2:39104200-39110600	Weak transcription	Fetal Stomach	stomach
33	chr2:39104200-39111000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:39104200-39111200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:39104200-39111200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr2:39104200-39111200	Weak transcription	Osteobl	bone
37	chr2:39104200-39111400	Weak transcription	HSMM	muscle
38	chr2:39104200-39111800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:39104200-39111800	Weak transcription	Fetal Kidney	kidney
40	chr2:39104200-39112000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:39104200-39112000	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:39104200-39112000	Weak transcription	NHDF-Ad	bronchial
43	chr2:39104200-39112200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr2:39104200-39112400	Weak transcription	Fetal Intestine Small	intestine
45	chr2:39104200-39112600	Weak transcription	Brain Angular Gyrus	brain
46	chr2:39104200-39112800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:39104200-39113400	Weak transcription	Fetal Intestine Large	intestine
48	chr2:39104200-39113400	Weak transcription	Psoas Muscle	Psoas
49	chr2:39104200-39113400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:39104200-39113800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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