Variant report

Variant	rs17396340
Chromosome Location	chr1:10286176-10286177
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:10285612-10286442	HepG2	liver:	n/a	n/a
2	SETDB1	chr1:10284546-10286332	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10284668..10286801-chr1:10289342..10292166,2	K562	blood:

Variant related genes	Relation type
KIF1B	TF binding region
MIR1273D	TF binding region
ENSG00000054523	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10864454	0.82[EUR][1000 genomes]
rs11121542	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11121548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11121556	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs12119075	1.00[CHB][hapmap]
rs12120465	0.83[EUR][1000 genomes]
rs12120499	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135219	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs12137527	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142043	0.84[EUR][1000 genomes]
rs17397129	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400878	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17401588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762289	0.84[EUR][1000 genomes]
rs4240912	0.86[EUR][1000 genomes]
rs4240913	0.86[EUR][1000 genomes]
rs4846204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846214	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4846217	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs58036267	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61383940	0.82[EUR][1000 genomes]
rs6670157	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6679596	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs6693965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6694081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6702280	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7525661	0.84[EUR][1000 genomes]
rs997482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]

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	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv999251	chr1:10276263-10318163	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Mean platelet volume	22139419	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17396340	KIF1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10272600-10368200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:10272800-10290000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:10272800-10296600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:10276800-10311800	Weak transcription	Hela-S3	cervix
5	chr1:10277000-10322000	Weak transcription	Spleen	Spleen
6	chr1:10278400-10291000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:10278400-10295200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:10278400-10302000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:10278600-10294800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:10278800-10292400	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:10278800-10296400	Weak transcription	Fetal Lung	lung
12	chr1:10279800-10297800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:10281000-10294800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:10282600-10291000	Weak transcription	Fetal Brain Female	brain
15	chr1:10283000-10288600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:10283600-10286200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr1:10283600-10287400	Enhancers	Left Ventricle	heart
18	chr1:10284000-10286800	Enhancers	Brain Substantia Nigra	brain
19	chr1:10284000-10287600	Enhancers	Brain Anterior Caudate	brain
20	chr1:10284000-10289200	Enhancers	Brain Hippocampus Middle	brain
21	chr1:10284400-10286200	Enhancers	Rectal Smooth Muscle	rectum
22	chr1:10284400-10286400	Enhancers	Right Ventricle	heart
23	chr1:10284400-10286800	Enhancers	Brain Cingulate Gyrus	brain
24	chr1:10284400-10287000	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr1:10284400-10289200	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr1:10284600-10286200	Enhancers	Muscle Satellite Cultured Cells	--
27	chr1:10284800-10286600	Enhancers	Osteobl	bone
28	chr1:10284800-10311000	Weak transcription	Small Intestine	intestine
29	chr1:10285000-10286200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:10285000-10286200	Enhancers	Ovary	ovary
31	chr1:10285000-10286200	Enhancers	NH-A	brain
32	chr1:10285000-10286400	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr1:10285000-10286400	Enhancers	HSMM	muscle
34	chr1:10285000-10286600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:10285000-10288400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:10285000-10289000	Enhancers	Colon Smooth Muscle	Colon
37	chr1:10285000-10294000	Weak transcription	Fetal Stomach	stomach
38	chr1:10285200-10286400	Enhancers	HSMMtube	muscle
39	chr1:10285200-10316000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:10285400-10287200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:10285400-10287400	Weak transcription	HepG2	liver
42	chr1:10285400-10292200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:10285400-10294000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:10285400-10302400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr1:10285400-10310800	Weak transcription	Aorta	Aorta
46	chr1:10285400-10312600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:10285600-10288400	Weak transcription	Stomach Mucosa	stomach
48	chr1:10285600-10288600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:10285600-10290000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:10285600-10290600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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