Variant report

Variant	rs55853078
Chromosome Location	chr3:160159899-160159900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160117555..160120667-chr3:160157707..160160444,3	MCF-7	breast:
2	chr3:160116116..160127665-chr3:160158037..160169627,42	K562	blood:
3	chr3:160158711..160161195-chr3:160357597..160359673,2	K562	blood:
4	chr3:160131023..160133383-chr3:160157352..160160209,3	K562	blood:
5	chr3:160152431..160159028-chr3:160159168..160164097,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207779	Chromatin interaction
ENSG00000198987	Chromatin interaction
ENSG00000068885	Chromatin interaction
ENSG00000113810	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1141023	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236389	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236452	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236487	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17826161	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882124	0.84[ASN][1000 genomes]
rs1882128	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1920648	0.84[ASN][1000 genomes]
rs1920654	0.84[ASN][1000 genomes]
rs1979160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2029361	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2152424	0.92[ASN][1000 genomes]
rs2272489	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35281166	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3737214	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41272955	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272957	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4254702	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4434183	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679883	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679887	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679894	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680577	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680582	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680590	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55930449	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56030166	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56051094	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56322040	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776582	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6780828	0.84[ASN][1000 genomes]
rs6806971	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73154549	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73154552	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154567	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73154591	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154600	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154602	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155920	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73155922	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73155924	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7622031	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826290	0.92[ASN][1000 genomes]
rs9845172	0.84[ASN][1000 genomes]
rs9847144	0.84[ASN][1000 genomes]
rs9876980	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55853078	HKDC1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160120200-160164400	Weak transcription	Fetal Brain Male	brain
2	chr3:160122000-160161000	Strong transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:160122000-160164400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:160122000-160164600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:160130000-160166200	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:160133800-160164600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:160140800-160166600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:160142400-160164400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:160143600-160166600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:160145600-160166800	Weak transcription	Right Atrium	heart
11	chr3:160146000-160160000	Weak transcription	Ovary	ovary
12	chr3:160146000-160162400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:160146000-160164400	Weak transcription	Gastric	stomach
14	chr3:160146000-160165400	Weak transcription	Aorta	Aorta
15	chr3:160146000-160167000	Weak transcription	Pancreas	Pancrea
16	chr3:160146400-160166200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:160146800-160160000	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:160147000-160164400	Weak transcription	Esophagus	oesophagus
19	chr3:160147000-160166200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:160147800-160164400	Weak transcription	Lung	lung
21	chr3:160150000-160160600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:160150000-160162400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:160150400-160162400	Weak transcription	Spleen	Spleen
24	chr3:160150600-160166000	Weak transcription	Fetal Brain Female	brain
25	chr3:160151000-160160600	Weak transcription	Fetal Kidney	kidney
26	chr3:160151000-160166600	Weak transcription	Small Intestine	intestine
27	chr3:160151000-160166800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:160152000-160160600	Weak transcription	HepG2	liver
29	chr3:160152200-160163600	Weak transcription	Brain Substantia Nigra	brain
30	chr3:160152200-160165200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:160152400-160164000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr3:160152400-160166000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:160152600-160165200	Weak transcription	Hela-S3	cervix
34	chr3:160152600-160166200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:160153200-160162400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:160153200-160166200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr3:160153400-160166600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:160154000-160163000	Weak transcription	HMEC	breast
39	chr3:160154000-160164600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr3:160154200-160162400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr3:160154200-160164400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr3:160154200-160165200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:160154200-160165400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:160154400-160162400	Weak transcription	Thymus	Thymus
45	chr3:160154400-160164400	Weak transcription	Brain Germinal Matrix	brain
46	chr3:160154600-160166400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:160155000-160165200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:160155000-160166600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:160155000-160167000	Weak transcription	Placenta	Placenta
50	chr3:160155200-160160200	Weak transcription	Fetal Intestine Small	intestine

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