Variant report

Variant	rs2039175
Chromosome Location	chr1:10587841-10587842
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10585162..10588309-chr1:10589608..10593566,5	K562	blood:
2	chr1:10586788..10588823-chr1:10605231..10607555,2	K562	blood:
3	chr1:10581501..10583988-chr1:10587081..10589695,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10157111	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10157119	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10746495	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10779739	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10779743	0.92[ASN][1000 genomes]
rs10779744	0.93[ASN][1000 genomes]
rs10864461	0.81[EUR][1000 genomes]
rs10864463	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11121584	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11121585	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11121588	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11121589	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11121593	0.93[ASN][1000 genomes]
rs11121594	0.93[ASN][1000 genomes]
rs12128630	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12133103	0.91[ASN][1000 genomes]
rs12565494	0.93[ASN][1000 genomes]
rs12750901	0.87[ASN][1000 genomes]
rs12753364	0.93[ASN][1000 genomes]
rs2039176	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2480771	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2480772	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2480773	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2480775	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2480780	0.81[EUR][1000 genomes]
rs2480781	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2480787	0.94[EUR][1000 genomes]
rs2480789	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2506878	0.91[EUR][1000 genomes]
rs2506888	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2506897	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2506898	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2506900	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2988398	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2988399	0.89[EUR][1000 genomes]
rs34230252	0.93[ASN][1000 genomes]
rs35409029	0.95[ASN][1000 genomes]
rs35612158	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4240914	0.81[EUR][1000 genomes]
rs4240915	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4617401	0.84[ASN][1000 genomes]
rs4845936	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4846230	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4846231	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4846232	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4846233	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4846237	0.91[ASN][1000 genomes]
rs61777207	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61777208	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6540937	0.93[ASN][1000 genomes]
rs6540938	0.93[ASN][1000 genomes]
rs6658073	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6661757	0.93[ASN][1000 genomes]
rs6663688	0.95[ASN][1000 genomes]
rs6663898	0.95[ASN][1000 genomes]
rs6664134	0.93[ASN][1000 genomes]
rs6681221	0.81[EUR][1000 genomes]
rs6687502	0.93[ASN][1000 genomes]
rs6687622	0.93[ASN][1000 genomes]
rs6700023	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6700886	0.91[ASN][1000 genomes]
rs710130	0.95[ASN][1000 genomes]
rs7519424	0.95[ASN][1000 genomes]
rs7524790	0.88[ASN][1000 genomes]
rs7534954	0.90[ASN][1000 genomes]
rs944191	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9660006	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9661121	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv2521	chr1:10553530-10598171	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv545395	chr1:10584672-10613660	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2039175	KIF1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10570800-10595600	Weak transcription	Primary B cells from cord blood	blood
2	chr1:10572000-10590000	Weak transcription	Spleen	Spleen
3	chr1:10572200-10598600	Weak transcription	Brain Anterior Caudate	brain
4	chr1:10573400-10596000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:10573800-10588000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:10573800-10588200	Weak transcription	Fetal Intestine Large	intestine
7	chr1:10575600-10588000	Weak transcription	NHLF	lung
8	chr1:10576000-10589200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr1:10576400-10596000	Weak transcription	Dnd41	blood
10	chr1:10577000-10603600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:10577400-10588000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:10577400-10588000	Weak transcription	Lung	lung
13	chr1:10577400-10588000	Weak transcription	NHDF-Ad	bronchial
14	chr1:10577400-10596400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:10577600-10588000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:10577600-10588400	Weak transcription	Adipose Nuclei	Adipose
17	chr1:10577800-10590800	Weak transcription	Fetal Thymus	thymus
18	chr1:10578000-10588000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:10578200-10588400	Weak transcription	Fetal Kidney	kidney
20	chr1:10578200-10589800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:10578400-10590600	Weak transcription	Placenta	Placenta
22	chr1:10579400-10589200	Weak transcription	Gastric	stomach
23	chr1:10579400-10610200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:10579600-10588000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:10579600-10590000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:10579600-10596200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:10579800-10588000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:10579800-10588000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:10579800-10588000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:10579800-10588000	Weak transcription	Esophagus	oesophagus
31	chr1:10579800-10588000	Weak transcription	HSMMtube	muscle
32	chr1:10579800-10588200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:10579800-10588200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:10579800-10588200	Weak transcription	Liver	Liver
35	chr1:10580000-10588000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:10580000-10588200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:10580000-10588200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:10580800-10588000	Weak transcription	Aorta	Aorta
39	chr1:10580800-10588000	Weak transcription	Fetal Intestine Small	intestine
40	chr1:10580800-10588000	Weak transcription	Fetal Stomach	stomach
41	chr1:10580800-10596000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:10580800-10596200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:10581600-10588000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:10582000-10588000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:10582200-10588200	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr1:10582600-10588000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:10582600-10588400	Weak transcription	Primary T cells from cord blood	blood
48	chr1:10582600-10595800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr1:10582600-10596200	Weak transcription	Thymus	Thymus
50	chr1:10582800-10588000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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