Variant report

Variant	rs2678070
Chromosome Location	chr5:118812180-118812181
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	chr5:118804681..118808687-chr5:118810812..118814012,4	K562	blood:

Variant related genes	Relation type
ENSG00000239084	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs2257901	0.94[ASN][1000 genomes]
rs2259347	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2451816	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2455463	0.85[ASN][1000 genomes]
rs2459726	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs246966	0.91[LWK][hapmap];0.89[YRI][hapmap]
rs25640	0.82[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs257971	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs257972	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs257973	0.82[CEU][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs257974	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs257975	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs257976	0.96[ASN][1000 genomes]
rs257978	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs26181	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.96[ASN][1000 genomes]
rs26184	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs2636961	0.91[CHD][hapmap]
rs2636964	1.00[CHB][hapmap]
rs2636968	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs27938	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs2945327	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs32640	0.86[ASN][1000 genomes]
rs32651	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32659	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs32662	0.88[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs32663	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs32664	0.94[ASN][1000 genomes]
rs32665	0.89[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35235684	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs382719	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs39970	0.94[ASN][1000 genomes]
rs39971	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs422297	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs426899	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[ASN][1000 genomes]
rs439954	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs442923	1.00[CHB][hapmap]
rs450118	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs455949	0.89[CEU][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap]
rs457106	0.93[CEU][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs460274	0.96[ASN][1000 genomes]
rs463513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs467076	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	nsv1030717	chr5:118709310-118836951	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2678070	HSD17B4	cis	brain	BrainEAC
rs2678070	HSD17B4	cis	parietal	SCAN
rs2678070	PRR16	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118789000-118813200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:118789000-118826800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr5:118789200-118813200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:118789400-118831200	Weak transcription	NH-A	brain
5	chr5:118789400-118831600	Weak transcription	HSMMtube	muscle
6	chr5:118789600-118813400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr5:118789600-118813600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr5:118789800-118813800	Weak transcription	Fetal Kidney	kidney
9	chr5:118789800-118814400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr5:118790000-118812600	Weak transcription	Fetal Brain Male	brain
11	chr5:118790200-118813400	Weak transcription	Aorta	Aorta
12	chr5:118791800-118846600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:118792400-118815000	Weak transcription	K562	blood
14	chr5:118793400-118812200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:118794800-118861200	Weak transcription	HSMM	muscle
16	chr5:118795200-118813400	Weak transcription	Small Intestine	intestine
17	chr5:118804200-118813600	Weak transcription	Colon Smooth Muscle	Colon
18	chr5:118804200-118879600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr5:118804400-118813000	Weak transcription	Colonic Mucosa	Colon
20	chr5:118804400-118813200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:118804400-118820000	Weak transcription	NHDF-Ad	bronchial
22	chr5:118804600-118813400	Weak transcription	Right Ventricle	heart
23	chr5:118804600-118818800	Weak transcription	Stomach Mucosa	stomach
24	chr5:118804600-118819400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr5:118804800-118813400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr5:118804800-118821400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr5:118804800-118837000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr5:118805200-118813400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr5:118805200-118839400	Weak transcription	NHEK	skin
30	chr5:118805400-118812800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr5:118805600-118813000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:118805600-118813400	Weak transcription	Fetal Muscle Leg	muscle
33	chr5:118805600-118817200	Weak transcription	Fetal Brain Female	brain
34	chr5:118805800-118813200	Weak transcription	Fetal Lung	lung
35	chr5:118805800-118817000	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr5:118805800-118829400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr5:118806000-118813400	Weak transcription	Fetal Intestine Small	intestine
38	chr5:118806000-118846400	Weak transcription	Esophagus	oesophagus
39	chr5:118806000-118846400	Weak transcription	Spleen	Spleen
40	chr5:118806200-118812800	Weak transcription	Lung	lung
41	chr5:118806200-118813000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:118806200-118813200	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr5:118806200-118813400	Weak transcription	Ovary	ovary
44	chr5:118806200-118813600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr5:118806200-118831400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr5:118806200-118844800	Weak transcription	Thymus	Thymus
47	chr5:118806200-118846400	Weak transcription	Pancreas	Pancrea
48	chr5:118806200-118855600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr5:118806400-118813200	Weak transcription	Gastric	stomach
50	chr5:118806400-118815200	Weak transcription	Hela-S3	cervix

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