Variant report

Variant	rs6656852
Chromosome Location	chr1:171752373-171752374
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr1:171749215-171752807	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr1:171749551-171752609	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:171749779..171754190-chr1:171762974..171767849,5	K562	blood:
2	chr1:171710341..171715416-chr1:171748571..171752440,7	MCF-7	breast:
3	chr1:171719352..171723049-chr1:171749265..171752646,3	MCF-7	breast:
4	chr1:171709343..171715185-chr1:171748592..171756289,15	K562	blood:
5	chr1:171708496..171713095-chr1:171747641..171752422,13	MCF-7	breast:

No data

Variant related genes	Relation type
METTL13	TF binding region
ENSG00000232261	Chromatin interaction
ENSG00000010165	Chromatin interaction
ENSG00000117533	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1045456	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10489252	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913683	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913684	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091786	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12565176	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12567851	0.87[EUR][1000 genomes]
rs12730717	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12742601	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12750330	0.88[EUR][1000 genomes]
rs12753043	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17596025	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17596081	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17649609	0.98[EUR][1000 genomes]
rs17650310	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17650340	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17657363	0.91[EUR][1000 genomes]
rs1801898	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2143369	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2181216	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2223602	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2232807	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232813	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232819	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232824	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232825	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs236894	0.81[EUR][1000 genomes]
rs236897	0.86[EUR][1000 genomes]
rs236898	0.86[EUR][1000 genomes]
rs236899	0.85[EUR][1000 genomes]
rs236900	0.87[EUR][1000 genomes]
rs34320898	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34627492	0.88[EUR][1000 genomes]
rs35249022	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35400839	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35631282	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35674909	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35882887	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35930163	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36080557	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3891278	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55732843	0.91[EUR][1000 genomes]
rs56365362	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56377810	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61807979	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6674364	0.98[EUR][1000 genomes]
rs6675708	0.98[EUR][1000 genomes]
rs6681322	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6689125	0.94[EUR][1000 genomes]
rs6695933	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7522582	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7536142	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6656852	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171749600-171752400	Active TSS	Rectal Smooth Muscle	rectum
2	chr1:171749800-171752400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:171749800-171752400	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr1:171749800-171752600	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr1:171751400-171752400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr1:171751400-171752600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr1:171751400-171754400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr1:171751400-171755000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:171751600-171752400	Enhancers	Primary hematopoietic stem cells	blood
10	chr1:171751600-171752400	Flanking Active TSS	Dnd41	blood
11	chr1:171751600-171752600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:171751600-171752600	Enhancers	Primary B cells from peripheral blood	blood
13	chr1:171751600-171752600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr1:171751600-171752800	Enhancers	Primary T cells fromperipheralblood	blood
15	chr1:171751600-171752800	Weak transcription	Left Ventricle	heart
16	chr1:171751600-171752800	Weak transcription	Lung	lung
17	chr1:171751600-171753000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:171751600-171753000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:171751600-171753000	Weak transcription	Esophagus	oesophagus
20	chr1:171751600-171753000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:171751600-171753000	Enhancers	Spleen	Spleen
22	chr1:171751600-171754800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:171751600-171770800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:171751800-171752400	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr1:171751800-171752400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr1:171751800-171752400	Enhancers	Fetal Stomach	stomach
27	chr1:171751800-171752400	Enhancers	Fetal Thymus	thymus
28	chr1:171751800-171752400	Flanking Active TSS	A549	lung
29	chr1:171751800-171752400	Flanking Active TSS	GM12878-XiMat	blood
30	chr1:171751800-171752400	Flanking Active TSS	Hela-S3	cervix
31	chr1:171751800-171752400	Transcr. at gene 5' and 3'	K562	blood
32	chr1:171751800-171752400	Transcr. at gene 5' and 3'	NHLF	lung
33	chr1:171751800-171752600	Enhancers	Primary T cells from cord blood	blood
34	chr1:171751800-171752600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr1:171751800-171752800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:171751800-171753000	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:171751800-171753200	Enhancers	Pancreas	Pancrea
38	chr1:171751800-171754200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:171752000-171752400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:171752000-171752400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:171752000-171752400	Enhancers	Adipose Nuclei	Adipose
42	chr1:171752000-171752400	Enhancers	Brain Hippocampus Middle	brain
43	chr1:171752000-171752400	Enhancers	Fetal Kidney	kidney
44	chr1:171752000-171752400	Genic enhancers	Fetal Muscle Leg	muscle
45	chr1:171752000-171752400	Enhancers	Stomach Smooth Muscle	stomach
46	chr1:171752000-171752600	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr1:171752000-171752600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:171752000-171752600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:171752000-171752600	Enhancers	Liver	Liver
50	chr1:171752000-171752600	Weak transcription	Brain Angular Gyrus	brain

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