Variant report

Variant	rs10461165
Chromosome Location	chr4:89770583-89770584
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:89757635..89759900-chr4:89769604..89772277,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1246642	0.83[CHD][hapmap]
rs12640274	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1379932	0.91[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs1379933	0.92[ASN][1000 genomes]
rs1458551	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2085600	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2446301	0.81[CHB][hapmap]
rs2464528	0.91[CHD][hapmap]
rs2609255	0.82[CHB][hapmap];0.88[CHD][hapmap];0.80[ASN][1000 genomes]
rs2609259	0.81[CHB][hapmap]
rs2609261	0.90[CHD][hapmap]
rs2609262	0.90[CHD][hapmap]
rs2609264	0.88[CHD][hapmap]
rs2869952	0.80[ASN][1000 genomes]
rs28767574	0.96[ASN][1000 genomes]
rs2904255	0.84[ASN][1000 genomes]
rs35019968	0.87[EUR][1000 genomes]
rs56158219	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6830970	0.82[CHD][hapmap]
rs71609539	0.87[EUR][1000 genomes]
rs73842248	0.87[EUR][1000 genomes]
rs73842249	0.85[EUR][1000 genomes]
rs7660000	0.95[GIH][hapmap];0.87[TSI][hapmap]
rs9991039	0.91[GIH][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10461165	HERC3	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89745000-89770800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:89745000-89775000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:89745200-89776200	Weak transcription	Aorta	Aorta
4	chr4:89752000-89778800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr4:89754600-89779600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr4:89764400-89779400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:89765000-89773200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:89765000-89779400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:89765000-89780400	Weak transcription	Ovary	ovary
10	chr4:89765000-89780600	Weak transcription	Left Ventricle	heart
11	chr4:89765200-89778200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:89765200-89780400	Weak transcription	Fetal Muscle Leg	muscle
13	chr4:89765400-89770600	Weak transcription	Placenta	Placenta
14	chr4:89765400-89780400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr4:89765400-89780800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr4:89766000-89773400	Weak transcription	Gastric	stomach
17	chr4:89766000-89780400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:89767600-89779800	Weak transcription	Fetal Stomach	stomach
19	chr4:89767800-89773000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:89767800-89775800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:89767800-89777600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:89767800-89779600	Weak transcription	Adipose Nuclei	Adipose
23	chr4:89767800-89780400	Weak transcription	Fetal Kidney	kidney
24	chr4:89767800-89780800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:89768000-89771400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:89768000-89775400	Weak transcription	Hela-S3	cervix
27	chr4:89768000-89779600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:89768600-89772600	Weak transcription	Fetal Intestine Large	intestine
29	chr4:89768800-89789400	Weak transcription	Fetal Intestine Small	intestine
30	chr4:89769200-89771000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr4:89769200-89771200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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