Variant report

Variant	rs56178029
Chromosome Location	chr1:171754164-171754165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr1:171754036-171754382	K562	blood:	n/a	n/a
2	POLR2A	chr1:171754160-171754257	HUVEC	blood vessel:	n/a	n/a
3	WRNIP1	chr1:171754056-171754191	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:171749779..171754190-chr1:171762974..171767849,5	K562	blood:
2	chr1:171712949..171715185-chr1:171753608..171756289,2	K562	blood:
3	chr1:171709343..171715185-chr1:171748592..171756289,15	K562	blood:
4	chr1:171754075..171756411-chr1:171764040..171766145,2	MCF-7	breast:

No data

Variant related genes	Relation type
METTL13	TF binding region
ENSG00000117533	Chromatin interaction
ENSG00000010165	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10798634	0.84[EUR][1000 genomes]
rs10798636	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10798667	0.90[ASN][1000 genomes]
rs10913644	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11587288	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11590059	0.81[AFR][1000 genomes]
rs11803889	0.84[AFR][1000 genomes]
rs12022693	0.81[AFR][1000 genomes]
rs12028128	0.84[EUR][1000 genomes]
rs12032340	0.84[EUR][1000 genomes]
rs12034454	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12039034	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12566700	0.91[ASN][1000 genomes]
rs16843385	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17597528	0.81[AFR][1000 genomes]
rs2232812	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232816	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2232818	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2232826	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2294717	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3753538	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56167663	0.84[AFR][1000 genomes]
rs57476157	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59302445	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60502293	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60956160	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6425405	0.84[EUR][1000 genomes]
rs6425423	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425428	0.81[AFR][1000 genomes]
rs6425438	0.90[ASN][1000 genomes]
rs6425439	0.89[ASN][1000 genomes]
rs6684594	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6691222	0.84[ASN][1000 genomes]
rs6692136	0.84[EUR][1000 genomes]
rs6695502	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72703115	0.90[ASN][1000 genomes]
rs7541192	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7542116	0.84[EUR][1000 genomes]
rs7543608	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7548462	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7551037	0.83[EUR][1000 genomes]
rs7860	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs909958	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs941942	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv522889	chr1:171749665-171755071	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv518222	chr1:171753039-171763549	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56178029	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171751400-171754400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr1:171751400-171755000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:171751600-171754800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:171751600-171770800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:171751800-171754200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:171752000-171754600	Weak transcription	HSMMtube	muscle
7	chr1:171752000-171754800	Weak transcription	Small Intestine	intestine
8	chr1:171752000-171755000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr1:171752000-171773600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:171752200-171755000	Weak transcription	Osteobl	bone
11	chr1:171752200-171759200	Weak transcription	Fetal Heart	heart
12	chr1:171752200-171762200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:171752200-171766600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:171752200-171767400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:171752200-171768200	Strong transcription	Fetal Muscle Trunk	muscle
16	chr1:171752400-171754200	Transcr. at gene 5' and 3'	Dnd41	blood
17	chr1:171752400-171754400	Weak transcription	Fetal Kidney	kidney
18	chr1:171752400-171754800	Genic enhancers	Duodenum Mucosa	Duodenum
19	chr1:171752400-171754800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:171752400-171754800	Weak transcription	HUVEC	blood vessel
21	chr1:171752400-171755400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:171752400-171755400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:171752400-171755400	Genic enhancers	K562	blood
24	chr1:171752400-171755600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:171752400-171766600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:171752400-171767200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:171752600-171754200	Genic enhancers	Primary T cells from cord blood	blood
28	chr1:171752600-171754200	Genic enhancers	Brain Angular Gyrus	brain
29	chr1:171752600-171754600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr1:171752600-171754600	Genic enhancers	Liver	Liver
31	chr1:171752600-171754600	Strong transcription	HSMM	muscle
32	chr1:171752600-171755000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:171752600-171755200	Genic enhancers	Stomach Smooth Muscle	stomach
34	chr1:171752600-171755600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
35	chr1:171752600-171756400	Strong transcription	NHEK	skin
36	chr1:171752600-171760000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:171752600-171767000	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:171752600-171767000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:171752600-171767400	Strong transcription	Primary B cells from cord blood	blood
40	chr1:171752600-171767400	Strong transcription	A549	lung
41	chr1:171752600-171767800	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr1:171752600-171767800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:171752800-171754200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:171752800-171754200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:171752800-171754200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:171752800-171754200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
47	chr1:171752800-171754200	Genic enhancers	Left Ventricle	heart
48	chr1:171752800-171754200	Genic enhancers	Psoas Muscle	Psoas
49	chr1:171752800-171754600	Genic enhancers	Primary B cells from peripheral blood	blood
50	chr1:171752800-171754800	Genic enhancers	Fetal Brain Female	brain

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