Variant report

Variant	rs340643
Chromosome Location	chr4:87947158-87947159
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:87924739..87931529-chr4:87944789..87955863,16	K562	blood:
2	chr4:87940559..87943450-chr4:87945338..87947892,3	K562	blood:
3	chr4:87944684..87947564-chr4:87957551..87959550,2	MCF-7	breast:
4	chr4:87945681..87948538-chr4:88025074..88026618,2	MCF-7	breast:
5	chr4:87855405..87858251-chr4:87947004..87950108,3	K562	blood:
6	chr4:87946350..87948006-chr4:87951593..87953106,2	MCF-7	breast:
7	chr4:87946215..87948894-chr4:88011118..88013120,2	MCF-7	breast:
8	chr4:87938501..87940925-chr4:87946524..87948135,2	K562	blood:
9	chr4:87855430..87859926-chr4:87946655..87949706,6	MCF-7	breast:
10	chr4:87944509..87947205-chr4:87948010..87950101,2	K562	blood:
11	chr4:87944178..87948145-chr4:87950244..87953545,6	K562	blood:
12	chr4:87944954..87950016-chr4:87950159..87955839,10	K562	blood:
13	chr4:87926004..87930134-chr4:87942000..87950091,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10015639	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10032244	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10516788	0.90[CEU][hapmap]
rs11729622	0.88[ASN][1000 genomes]
rs13126334	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13127250	0.89[ASN][1000 genomes]
rs151451	0.82[CEU][hapmap]
rs17012234	0.90[CEU][hapmap]
rs17701999	0.90[CEU][hapmap]
rs17752307	0.90[CEU][hapmap]
rs2007132	0.94[ASN][1000 genomes]
rs2053769	0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2053770	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs340626	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs340630	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs340633	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs340636	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs340637	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs340638	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs340639	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[ASN][1000 genomes]
rs340641	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs340642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs340648	0.92[ASN][1000 genomes]
rs340650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs340651	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs375795	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs388401	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4386567	0.80[ASN][1000 genomes]
rs443459	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4693798	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4693800	0.89[ASN][1000 genomes]
rs58633957	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6531941	0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs6531946	0.90[ASN][1000 genomes]
rs6531948	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6811587	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6819155	0.90[CEU][hapmap]
rs6839933	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6840258	0.89[CEU][hapmap]
rs6854749	0.90[CEU][hapmap]
rs7657530	0.82[CHB][hapmap]
rs7665282	0.90[CEU][hapmap]
rs767315	0.84[CEU][hapmap]
rs7682652	0.90[CEU][hapmap]
rs867196	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9715807	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription 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	25 gene(s)	inside rSNPs	diseases
8	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs340643	HSD17B13	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87930600-87950000	Weak transcription	Fetal Stomach	stomach
2	chr4:87935600-87950200	Weak transcription	Fetal Muscle Leg	muscle
3	chr4:87935800-87951000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr4:87936000-87950000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:87937000-87950400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:87937000-87951800	Weak transcription	NHEK	skin
7	chr4:87937000-87952000	Weak transcription	HMEC	breast
8	chr4:87937600-87949800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:87939400-87950800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:87939600-87950000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:87939600-87950400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:87940600-87950600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:87942600-87947600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr4:87942600-87950400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr4:87943000-87947600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr4:87943000-87948800	Enhancers	Small Intestine	intestine
17	chr4:87943200-87951400	Weak transcription	Fetal Brain Male	brain
18	chr4:87944000-87949200	Enhancers	Ovary	ovary
19	chr4:87944200-87948000	Enhancers	Psoas Muscle	Psoas
20	chr4:87944200-87949000	Enhancers	Liver	Liver
21	chr4:87944200-87951800	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr4:87944200-87951800	Enhancers	K562	blood
23	chr4:87944200-87953000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:87944200-87960800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:87944400-87948600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr4:87944600-87948600	Enhancers	Adipose Nuclei	Adipose
27	chr4:87944800-87947800	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr4:87944800-87947800	Enhancers	Brain Substantia Nigra	brain
29	chr4:87944800-87948000	Enhancers	HepG2	liver
30	chr4:87944800-87948600	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr4:87944800-87948800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr4:87944800-87948800	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr4:87944800-87948800	Enhancers	Stomach Mucosa	stomach
34	chr4:87944800-87949200	Enhancers	Right Ventricle	heart
35	chr4:87944800-87961600	Enhancers	Fetal Heart	heart
36	chr4:87945000-87947600	Weak transcription	Thymus	Thymus
37	chr4:87945000-87948600	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr4:87945000-87951800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr4:87945200-87947200	Enhancers	H1 Cell Line	embryonic stem cell
40	chr4:87945200-87948000	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr4:87945200-87948000	Enhancers	Left Ventricle	heart
42	chr4:87945200-87948600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:87945200-87948600	Enhancers	Spleen	Spleen
44	chr4:87945400-87947600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr4:87945400-87950000	Weak transcription	Aorta	Aorta
46	chr4:87945400-87951200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:87945600-87947400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr4:87945600-87947600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:87945600-87947600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr4:87945600-87947800	Weak transcription	Primary T cells from cord blood	blood

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