Variant report

Variant	rs17476234
Chromosome Location	chr3:47326298-47326299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47321055..47325957-chr3:47326199..47329332,5	MCF-7	breast:
2	chr3:47323698..47326869-chr3:47421986..47424400,3	MCF-7	breast:
3	chr3:47326087..47329023-chr3:47353816..47355413,2	K562	blood:

Variant related genes	Relation type
ENSG00000260236	Chromatin interaction
ENSG00000088727	Chromatin interaction
ENSG00000076201	Chromatin interaction
ENSG00000114648	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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130123	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130124	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11130126	0.87[EUR][1000 genomes]
rs11710013	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11710121	0.82[AFR][1000 genomes]
rs11710322	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714294	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11915074	0.87[EUR][1000 genomes]
rs11920853	0.87[EUR][1000 genomes]
rs11921117	0.85[EUR][1000 genomes]
rs13072802	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13094438	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1638676	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276853	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2276854	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs295428	0.80[ASN][1000 genomes]
rs295441	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295442	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683326	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59689369	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6768221	0.87[EUR][1000 genomes]
rs6791842	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7636423	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs807932	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs807935	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs807936	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs807937	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs811115	0.98[EUR][1000 genomes];0.99[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
rs17476234	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs17476234	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47324800-47327200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr3:47325000-47328400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr3:47325200-47326800	Enhancers	Small Intestine	intestine
4	chr3:47325400-47361000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:47325600-47326400	Enhancers	Primary T cells from cord blood	blood
6	chr3:47325600-47326400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:47325600-47326400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr3:47325600-47326400	Enhancers	Fetal Muscle Leg	muscle
9	chr3:47325600-47326400	Enhancers	Stomach Mucosa	stomach
10	chr3:47325600-47326600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:47325600-47326600	Enhancers	Liver	Liver
12	chr3:47325600-47326600	Enhancers	Fetal Muscle Trunk	muscle
13	chr3:47325600-47326600	Enhancers	Left Ventricle	heart
14	chr3:47325600-47326800	Enhancers	Duodenum Mucosa	Duodenum
15	chr3:47325600-47327000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr3:47325600-47327000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:47325600-47327000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:47325600-47327000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr3:47325600-47327000	Enhancers	Brain Angular Gyrus	brain
20	chr3:47325600-47327000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr3:47325600-47327200	Enhancers	Brain Hippocampus Middle	brain
22	chr3:47325600-47327400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr3:47325600-47327400	Enhancers	Brain Cingulate Gyrus	brain
24	chr3:47325600-47327400	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr3:47325600-47328000	Enhancers	Primary B cells from peripheral blood	blood
26	chr3:47325600-47328000	Weak transcription	Thymus	Thymus
27	chr3:47325600-47328200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:47325600-47328200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:47325600-47328400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:47325600-47328600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:47325600-47328600	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr3:47325600-47328600	Enhancers	Colon Smooth Muscle	Colon
33	chr3:47325600-47328600	Weak transcription	HSMMtube	muscle
34	chr3:47325600-47328800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr3:47325600-47328800	Weak transcription	Psoas Muscle	Psoas
36	chr3:47325600-47330400	Weak transcription	Colonic Mucosa	Colon
37	chr3:47325600-47331200	Weak transcription	Aorta	Aorta
38	chr3:47325600-47332000	Weak transcription	Esophagus	oesophagus
39	chr3:47325600-47334200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:47325600-47334400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:47325600-47334400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr3:47325600-47337800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr3:47325600-47338000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr3:47325600-47344600	Weak transcription	Ovary	ovary
45	chr3:47325600-47367600	Weak transcription	A549	lung
46	chr3:47325800-47326400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:47325800-47326400	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr3:47325800-47326400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:47325800-47326400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:47325800-47326600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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