Variant report

Variant	rs55843455
Chromosome Location	chr3:47008013-47008014
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46986447..46988013-chr3:47007335..47010204,2	MCF-7	breast:
2	chr3:47004144..47011042-chr3:47018115..47025018,10	MCF-7	breast:
3	chr3:47006914..47008838-chr3:47035650..47037247,2	MCF-7	breast:
4	chr3:46970325..46973197-chr3:47005456..47008384,2	MCF-7	breast:
5	chr3:47007836..47011318-chr3:47011441..47014509,4	MCF-7	breast:
6	chr3:47000539..47004616-chr3:47005854..47010349,8	K562	blood:

Variant related genes	Relation type
ENSG00000160799	Chromatin interaction
ENSG00000160796	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10433549	0.87[EUR][1000 genomes]
rs10461018	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1079276	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1108301	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11130110	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130111	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130112	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11707736	0.80[EUR][1000 genomes]
rs11709660	0.81[EUR][1000 genomes]
rs11715121	0.81[EUR][1000 genomes]
rs11716553	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11720139	0.88[EUR][1000 genomes]
rs11917361	0.83[EUR][1000 genomes]
rs11917474	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12152493	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12491473	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12630534	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12715421	0.82[EUR][1000 genomes]
rs13062681	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13066214	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13077398	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13091054	0.86[EUR][1000 genomes]
rs1463393	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17784127	0.85[EUR][1000 genomes]
rs1869869	0.98[EUR][1000 genomes]
rs1869871	0.90[EUR][1000 genomes]
rs2061197	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2278963	0.88[EUR][1000 genomes]
rs2305634	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2305635	0.88[EUR][1000 genomes]
rs2305638	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2385867	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34103310	0.88[EUR][1000 genomes]
rs34344887	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4078466	0.84[EUR][1000 genomes]
rs4082155	0.84[EUR][1000 genomes]
rs4234465	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4682831	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4682837	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682844	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4683322	0.81[EUR][1000 genomes]
rs55724164	0.83[EUR][1000 genomes]
rs55927279	0.82[EUR][1000 genomes]
rs56217494	0.85[EUR][1000 genomes]
rs56249396	0.83[EUR][1000 genomes]
rs61729713	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62246375	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62246398	0.83[EUR][1000 genomes]
rs62248439	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6442055	0.81[EUR][1000 genomes]
rs66539935	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66564457	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6763236	0.87[EUR][1000 genomes]
rs6767218	0.83[EUR][1000 genomes]
rs6768722	0.81[EUR][1000 genomes]
rs6774733	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6777145	0.81[EUR][1000 genomes]
rs6794193	0.86[EUR][1000 genomes]
rs6808742	0.90[EUR][1000 genomes]
rs749511	0.88[EUR][1000 genomes]
rs7610636	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7617689	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7625067	0.88[EUR][1000 genomes]
rs7625070	0.88[EUR][1000 genomes]
rs7628747	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7633698	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7636252	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7637302	0.85[EUR][1000 genomes]
rs7640397	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9844122	0.80[EUR][1000 genomes]
rs9845728	0.80[EUR][1000 genomes]
rs9854790	0.81[EUR][1000 genomes]
rs9858443	0.82[EUR][1000 genomes]
rs9875235	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS 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	25 gene(s)	inside rSNPs	diseases
4	nsv1012682	chr3:46973552-47016357	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55843455	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs55843455	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47002200-47012000	Weak transcription	Osteobl	bone
2	chr3:47002400-47012000	Weak transcription	NHLF	lung
3	chr3:47002400-47013200	Weak transcription	NH-A	brain
4	chr3:47003000-47010400	Weak transcription	Aorta	Aorta
5	chr3:47003200-47011800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:47003200-47012000	Weak transcription	Brain Angular Gyrus	brain
7	chr3:47003200-47012000	Weak transcription	NHDF-Ad	bronchial
8	chr3:47003200-47015800	Weak transcription	Fetal Brain Male	brain
9	chr3:47003200-47016800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:47003400-47008600	Weak transcription	Brain Substantia Nigra	brain
11	chr3:47003400-47012000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:47004400-47011800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:47004800-47011800	Weak transcription	HUVEC	blood vessel
14	chr3:47004800-47012000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:47004800-47012600	Weak transcription	HSMM	muscle
16	chr3:47004800-47017200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:47004800-47017200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:47005000-47008400	Weak transcription	HMEC	breast
19	chr3:47005600-47008400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr3:47006400-47009600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:47006400-47010600	Genic enhancers	Primary hematopoietic stem cells	blood
22	chr3:47006400-47011200	Enhancers	Liver	Liver
23	chr3:47006400-47011400	Genic enhancers	HepG2	liver
24	chr3:47006400-47012600	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr3:47006400-47013000	Genic enhancers	K562	blood
26	chr3:47006400-47013200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:47006400-47013600	Genic enhancers	Fetal Intestine Small	intestine
28	chr3:47006600-47008200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr3:47006600-47008800	Strong transcription	Brain Germinal Matrix	brain
30	chr3:47006600-47009000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
31	chr3:47006600-47009400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr3:47006600-47009400	Enhancers	Placenta	Placenta
33	chr3:47006600-47010000	Enhancers	Placenta Amnion	Placenta Amnion
34	chr3:47006600-47010000	Genic enhancers	NHEK	skin
35	chr3:47006600-47010400	Genic enhancers	GM12878-XiMat	blood
36	chr3:47006600-47011200	Genic enhancers	Stomach Smooth Muscle	stomach
37	chr3:47006600-47011400	Enhancers	Stomach Mucosa	stomach
38	chr3:47006600-47013200	Strong transcription	Dnd41	blood
39	chr3:47006600-47013400	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr3:47006600-47014400	Genic enhancers	Fetal Thymus	thymus
41	chr3:47006600-47017000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr3:47006800-47008800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:47006800-47008800	Enhancers	Small Intestine	intestine
44	chr3:47006800-47009200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:47006800-47009200	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr3:47006800-47009400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:47006800-47010800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:47006800-47012600	Genic enhancers	Primary B cells from cord blood	blood
49	chr3:47006800-47013200	Genic enhancers	Esophagus	oesophagus
50	chr3:47006800-47013600	Genic enhancers	Lung	lung

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