Variant report

Variant	rs732305
Chromosome Location	chr1:171754799-171754800
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr1:171754637-171754838	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr1:171754660-171754906	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr1:171754597-171754904	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr1:171754411-171754917	MCF10A-Er-Src	breast:	n/a	chr1:171754502-171754509
5	STAT3	chr1:171754636-171754906	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr1:171754662-171754838	MCF10A-Er-Src	breast:	n/a	n/a

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

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

Extended variants
information (count: 122 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10158220	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10158235	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10158943	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10159080	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10489253	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10753190	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753195	0.87[ASN][1000 genomes]
rs10753196	0.87[ASN][1000 genomes]
rs10753197	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10753198	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1079820	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10798637	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10798657	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10798658	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10798661	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10798679	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913633	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10913639	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10913651	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10913730	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10913743	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913799	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10913803	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11579138	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11580187	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11585645	0.87[ASN][1000 genomes]
rs11588649	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11589200	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11589823	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11590059	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11590829	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11807195	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12022693	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12022753	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12031686	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035109	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12036580	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12057976	0.82[ASN][1000 genomes]
rs12063769	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12562644	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12723938	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12735285	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12754084	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12755791	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1555101	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555102	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17597528	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17597542	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2206541	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2206542	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2232804	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232809	0.92[ASN][1000 genomes]
rs2232811	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294720	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294721	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294722	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421912	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2421913	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34219132	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35738870	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4292987	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55739261	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59592673	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6425416	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425417	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425422	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425428	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6425435	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6425436	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6425437	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6425440	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6425441	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6656814	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6657803	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6658116	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6658730	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6658980	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6659621	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6665727	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6668165	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6674810	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6675011	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6678230	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6682147	0.87[ASN][1000 genomes]
rs6685030	0.89[ASN][1000 genomes]
rs6689108	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6689213	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6690544	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6695736	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6698366	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6698467	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6698892	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6700184	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6700384	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6702424	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs732304	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517546	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7517555	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7520688	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs752514	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525313	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7537173	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7537770	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7537931	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7537935	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7539505	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7541128	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7542691	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7545100	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7549347	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7550603	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7552369	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556602	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs764179	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs764180	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs909959	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][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
rs732305	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	chr1:171751400-171755000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:171751600-171754800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:171751600-171770800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:171752000-171754800	Weak transcription	Small Intestine	intestine
5	chr1:171752000-171755000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr1:171752000-171773600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:171752200-171755000	Weak transcription	Osteobl	bone
8	chr1:171752200-171759200	Weak transcription	Fetal Heart	heart
9	chr1:171752200-171762200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:171752200-171766600	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:171752200-171767400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:171752200-171768200	Strong transcription	Fetal Muscle Trunk	muscle
13	chr1:171752400-171754800	Genic enhancers	Duodenum Mucosa	Duodenum
14	chr1:171752400-171754800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:171752400-171754800	Weak transcription	HUVEC	blood vessel
16	chr1:171752400-171755400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:171752400-171755400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:171752400-171755400	Genic enhancers	K562	blood
19	chr1:171752400-171755600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:171752400-171766600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:171752400-171767200	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:171752600-171755000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:171752600-171755200	Genic enhancers	Stomach Smooth Muscle	stomach
24	chr1:171752600-171755600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
25	chr1:171752600-171756400	Strong transcription	NHEK	skin
26	chr1:171752600-171760000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:171752600-171767000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:171752600-171767000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:171752600-171767400	Strong transcription	Primary B cells from cord blood	blood
30	chr1:171752600-171767400	Strong transcription	A549	lung
31	chr1:171752600-171767800	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr1:171752600-171767800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:171752800-171754800	Genic enhancers	Fetal Brain Female	brain
34	chr1:171752800-171755400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr1:171752800-171755400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr1:171752800-171755400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:171752800-171755400	Genic enhancers	Lung	lung
38	chr1:171752800-171755600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
39	chr1:171752800-171755800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:171752800-171756000	Genic enhancers	Primary T cells fromperipheralblood	blood
41	chr1:171752800-171756000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:171752800-171757200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:171752800-171757800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:171752800-171761800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
45	chr1:171752800-171762600	Strong transcription	Fetal Stomach	stomach
46	chr1:171752800-171765800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:171752800-171766600	Strong transcription	Placenta	Placenta
48	chr1:171752800-171767200	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr1:171752800-171770200	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr1:171753000-171755000	Genic enhancers	Sigmoid Colon	Sigmoid Colon

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