Variant report

Variant	rs17701999
Chromosome Location	chr4:87955544-87955545
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87924739..87931529-chr4:87944789..87955863,16	K562	blood:
2	chr4:87953334..87957046-chr4:87958598..87961763,4	K562	blood:
3	chr4:87944954..87950016-chr4:87950159..87955839,10	K562	blood:
4	chr4:87927091..87929349-chr4:87954392..87957373,2	MCF-7	breast:
5	chr4:87926472..87930256-chr4:87951394..87957719,6	K562	blood:
6	chr4:87950378..87952064-chr4:87953827..87955577,2	MCF-7	breast:
7	chr4:87952663..87956832-chr4:87958320..87961763,4	K562	blood:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10023056	0.90[CEU][hapmap]
rs10032244	0.90[CEU][hapmap]
rs10032710	0.90[CEU][hapmap];0.88[GIH][hapmap];0.80[TSI][hapmap]
rs10516785	0.85[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs10516786	0.80[ASW][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap]
rs10516788	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1471251	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs151451	0.94[CEU][hapmap]
rs17012200	0.85[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap];0.81[ASN][1000 genomes]
rs17012213	0.81[ASN][1000 genomes]
rs17012234	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17012334	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs17604480	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17751557	0.80[TSI][hapmap]
rs17752307	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1842685	0.90[CEU][hapmap];0.88[GIH][hapmap];0.80[TSI][hapmap]
rs2061498	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs236676	0.84[CEU][hapmap];0.94[GIH][hapmap];0.80[TSI][hapmap]
rs340633	0.85[CEU][hapmap]
rs340637	0.90[CEU][hapmap]
rs340638	0.90[CEU][hapmap]
rs340642	0.90[CEU][hapmap]
rs340643	0.90[CEU][hapmap]
rs340650	0.90[CEU][hapmap]
rs3733377	0.90[CEU][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap]
rs3736668	0.84[CEU][hapmap]
rs3755980	0.84[CEU][hapmap];0.94[GIH][hapmap];0.80[TSI][hapmap]
rs4693795	0.83[JPT][hapmap]
rs4693801	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4693802	0.94[GIH][hapmap];0.85[TSI][hapmap]
rs55787557	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55816619	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55879154	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55913164	0.82[ASN][1000 genomes]
rs55982755	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56023922	0.83[ASN][1000 genomes]
rs56050898	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56201818	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56378441	0.81[ASN][1000 genomes]
rs56390363	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56395939	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56406125	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6531941	0.80[TSI][hapmap]
rs6819155	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6839933	0.89[CEU][hapmap]
rs6840258	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6854749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72667735	0.81[ASN][1000 genomes]
rs72667736	0.81[ASN][1000 genomes]
rs72667737	0.81[ASN][1000 genomes]
rs72667739	0.81[ASN][1000 genomes]
rs72667747	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72667748	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72667750	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72667751	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72667752	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72667753	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72667754	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72667757	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72667759	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72667765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7665282	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs767315	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7682652	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7695426	0.86[EUR][1000 genomes];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
rs17701999	HSD17B13	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87944200-87960800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr4:87944800-87961600	Enhancers	Fetal Heart	heart
3	chr4:87947800-87957200	Weak transcription	Dnd41	blood
4	chr4:87949200-87957400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr4:87949200-87961000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr4:87949400-87960600	Enhancers	Liver	Liver
7	chr4:87949600-87955600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:87949600-87960800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr4:87949800-87957400	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr4:87949800-87960800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr4:87950000-87955600	Enhancers	Fetal Stomach	stomach
12	chr4:87950000-87955600	Enhancers	Small Intestine	intestine
13	chr4:87950000-87955800	Enhancers	Fetal Intestine Small	intestine
14	chr4:87950000-87958600	Enhancers	Psoas Muscle	Psoas
15	chr4:87950000-87960200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:87950200-87955800	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr4:87950200-87962600	Enhancers	Fetal Muscle Leg	muscle
18	chr4:87950400-87955600	Enhancers	Fetal Kidney	kidney
19	chr4:87950600-87955600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:87951000-87957800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr4:87951200-87956000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:87951200-87956400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:87951600-87956400	Enhancers	Stomach Mucosa	stomach
24	chr4:87951600-87959000	Enhancers	Fetal Intestine Large	intestine
25	chr4:87951800-87955600	Enhancers	HepG2	liver
26	chr4:87951800-87956000	Enhancers	NH-A	brain
27	chr4:87951800-87960400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr4:87952000-87956200	Enhancers	HMEC	breast
29	chr4:87952200-87957000	Weak transcription	Thymus	Thymus
30	chr4:87952400-87955800	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr4:87952400-87956000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr4:87952400-87956200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr4:87952400-87956800	Weak transcription	Fetal Thymus	thymus
34	chr4:87952400-87957600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:87952400-87957600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr4:87952400-87960000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:87952400-87960400	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr4:87952400-87967000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr4:87952600-87958800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:87952600-87961000	Enhancers	K562	blood
41	chr4:87952600-87968000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:87952800-87961000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr4:87953000-87955800	Enhancers	Right Ventricle	heart
44	chr4:87953000-87960800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:87953400-87955600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr4:87953400-87956400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr4:87953400-87957600	Weak transcription	Fetal Brain Female	brain
48	chr4:87953400-87958800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr4:87953400-87965800	Weak transcription	Primary T cells from cord blood	blood
50	chr4:87953400-87967600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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