Variant report

Variant	rs807935
Chromosome Location	chr3:47321669-47321670
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	chr3:47321384-47325284	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:47321391-47322072	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:47321404-47322010	K562	blood:	n/a	n/a
4	POLR2A	chr3:47321218-47324899	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47204122..47207133-chr3:47321636..47325818,4	K562	blood:

Variant related genes	Relation type
KLHL18	TF binding region
KIF9	TF binding region
ENSG00000181555	Chromatin interaction
ENSG00000227398	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1076394	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130123	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11130124	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130126	0.85[EUR][1000 genomes]
rs11710013	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11710322	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11714294	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11915074	0.85[EUR][1000 genomes]
rs11920853	0.85[EUR][1000 genomes]
rs11921117	0.84[EUR][1000 genomes]
rs13072802	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13094438	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1638676	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17476234	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276853	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2276854	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs295428	0.81[AFR][1000 genomes]
rs295441	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs295442	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs295461	0.81[AFR][1000 genomes]
rs4683326	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59689369	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6768221	0.85[EUR][1000 genomes]
rs6791842	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7636423	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs807932	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs807936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs807937	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs811115	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs807935	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs807935	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47264200-47322200	Weak transcription	Gastric	stomach
2	chr3:47282800-47322400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:47293600-47323200	Weak transcription	Spleen	Spleen
4	chr3:47300800-47322800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:47301000-47322800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:47301200-47323000	Weak transcription	Psoas Muscle	Psoas
7	chr3:47302600-47322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:47302800-47323200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:47305600-47323200	Weak transcription	Primary T cells from cord blood	blood
10	chr3:47308600-47322200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:47308600-47322400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:47308600-47323000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:47308600-47323200	Weak transcription	Esophagus	oesophagus
14	chr3:47308800-47322200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:47308800-47322200	Weak transcription	Hela-S3	cervix
16	chr3:47308800-47322200	Weak transcription	HepG2	liver
17	chr3:47308800-47322200	Weak transcription	NHEK	skin
18	chr3:47308800-47322400	Weak transcription	A549	lung
19	chr3:47308800-47322600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:47308800-47322600	Weak transcription	Brain Anterior Caudate	brain
21	chr3:47308800-47322600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:47308800-47322800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:47308800-47322800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:47308800-47323000	Weak transcription	Adipose Nuclei	Adipose
25	chr3:47308800-47323000	Weak transcription	Brain Substantia Nigra	brain
26	chr3:47309000-47322200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:47309000-47322200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:47309000-47322400	Weak transcription	Placenta	Placenta
29	chr3:47309000-47322600	Weak transcription	HUVEC	blood vessel
30	chr3:47309000-47322800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:47309000-47322800	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:47309000-47323000	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:47309000-47323200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:47309000-47323200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:47309200-47322200	Weak transcription	K562	blood
36	chr3:47309200-47322600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:47309200-47323200	Weak transcription	HSMMtube	muscle
38	chr3:47309800-47322200	Weak transcription	Dnd41	blood
39	chr3:47311000-47322800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:47311600-47322200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:47311600-47322400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:47311600-47322400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:47312000-47322400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:47312400-47323000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:47312600-47322600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr3:47312600-47322800	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr3:47314800-47323200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr3:47315200-47322400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr3:47315200-47322400	Weak transcription	Right Ventricle	heart
50	chr3:47315600-47322600	Weak transcription	Fetal Intestine Large	intestine

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