Variant report

Variant	rs3850202
Chromosome Location	chr5:118878872-118878873
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	chr5:118872062..118875418-chr5:118875456..118880778,4	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10042168	0.83[CHB][hapmap]
rs10045066	0.83[CHB][hapmap]
rs10051019	0.83[CHB][hapmap]
rs10069875	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs10073818	0.82[CHB][hapmap]
rs10078097	0.84[CHB][hapmap]
rs10478426	0.83[CHB][hapmap]
rs11241506	0.82[CHB][hapmap]
rs12653056	0.83[CHB][hapmap]
rs12653702	0.84[CHB][hapmap]
rs13361193	0.84[CHB][hapmap]
rs2075698	0.83[CHB][hapmap]
rs2257900	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2257901	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2259347	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2287712	0.84[CHB][hapmap]
rs2303003	0.84[CHB][hapmap]
rs2451816	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2459726	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs246965	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs246967	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2546210	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs25640	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs257970	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs257971	0.85[ASN][1000 genomes]
rs257972	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs257973	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs257974	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs26180	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs26181	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs26184	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2636961	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2636962	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2636964	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2636968	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2678074	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2678076	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2678091	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs27938	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2945327	0.96[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs32659	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs32662	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs32663	0.85[ASN][1000 genomes]
rs32664	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs32665	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs35235684	0.87[ASN][1000 genomes]
rs3797363	0.83[CHB][hapmap]
rs3797367	0.83[CHB][hapmap]
rs382719	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs3850200	0.83[CHB][hapmap]
rs39970	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs422297	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs426899	0.81[CEU][hapmap]
rs455949	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs457106	0.87[CHB][hapmap]
rs460274	0.85[EUR][1000 genomes]
rs461108	0.86[CHB][hapmap]
rs463098	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs465091	0.87[CHB][hapmap]
rs4895372	0.87[CHB][hapmap]
rs6875595	0.86[CHB][hapmap]
rs6894991	0.83[CHB][hapmap]
rs6895345	0.83[CHB][hapmap]
rs7721602	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1016271	chr5:118836891-119487982	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv882776	chr5:118859546-118915408	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv882777	chr5:118870452-118981480	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3850202	HSD17B4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118804200-118879600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:118841000-118880000	Weak transcription	Brain Germinal Matrix	brain
3	chr5:118841200-118880000	Weak transcription	A549	lung
4	chr5:118847200-118879800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:118847400-118879800	Weak transcription	HSMMtube	muscle
6	chr5:118847600-118879800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr5:118853000-118880200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:118854400-118879600	Weak transcription	Fetal Kidney	kidney
9	chr5:118854400-118880600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr5:118860600-118879200	Strong transcription	Liver	Liver
11	chr5:118861400-118879800	Weak transcription	HepG2	liver
12	chr5:118862000-118879800	Weak transcription	HSMM	muscle
13	chr5:118862000-118880200	Weak transcription	Fetal Lung	lung
14	chr5:118863600-118879200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:118864200-118879800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:118864200-118880200	Weak transcription	Colon Smooth Muscle	Colon
17	chr5:118864400-118880200	Weak transcription	Fetal Brain Female	brain
18	chr5:118865800-118879400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:118866000-118883200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr5:118866400-118879800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr5:118866400-118880000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr5:118869400-118880000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:118869600-118880000	Weak transcription	K562	blood
24	chr5:118871800-118879000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:118872000-118879000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:118872000-118879000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:118873200-118879000	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr5:118873200-118879200	Strong transcription	Adipose Nuclei	Adipose
29	chr5:118873400-118879200	Strong transcription	Primary B cells from cord blood	blood
30	chr5:118874000-118879200	Weak transcription	HUVEC	blood vessel
31	chr5:118874400-118879000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:118874400-118880000	Weak transcription	Fetal Brain Male	brain
33	chr5:118874400-118880200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:118874400-118880400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:118874600-118879800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr5:118874600-118880000	Weak transcription	GM12878-XiMat	blood
37	chr5:118874600-118880400	Weak transcription	Fetal Muscle Leg	muscle
38	chr5:118874800-118890200	Weak transcription	Fetal Heart	heart
39	chr5:118875000-118880000	Weak transcription	Brain Hippocampus Middle	brain
40	chr5:118875600-118879000	Strong transcription	Pancreas	Pancrea
41	chr5:118875800-118879200	Strong transcription	Left Ventricle	heart
42	chr5:118875800-118879400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:118876400-118879000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:118876400-118879000	Strong transcription	Lung	lung
45	chr5:118876400-118881000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr5:118876600-118880600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr5:118876800-118879000	Strong transcription	Placenta	Placenta
48	chr5:118877000-118879200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:118877200-118879000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr5:118877200-118880200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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