Variant report

Variant	rs6429609
Chromosome Location	chr1:47187496-47187497
allele	A/C
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	GATA3	chr1:47187491-47187752	T-47D	breast:	n/a	n/a
2	HDAC2	chr1:47187409-47187821	MCF-7	breast:	n/a	chr1:47187659-47187668
3	GATA3	chr1:47187446-47187984	MCF-7	breast:	n/a	chr1:47187751-47187761
4	FOXA1	chr1:47187479-47187784	HepG2	liver:	n/a	n/a
5	RCOR1	chr1:47187474-47187844	K562	blood:	n/a	n/a
6	GATA3	chr1:47187403-47187825	MCF-7	breast:	n/a	chr1:47187751-47187761
7	GATA3	chr1:47187488-47187897	MCF-7	breast:	n/a	chr1:47187751-47187761
8	MAZ	chr1:47187420-47187783	K562	blood:	n/a	n/a
9	UBTF	chr1:47187421-47187737	K562	blood:	n/a	n/a
10	POLR2A	chr1:47187437-47187571	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47068203..47069866-chr1:47187301..47190738,3	MCF-7	breast:

Variant related genes	Relation type
EFCAB14	TF binding region

Extended variants
information (count: 124 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10158678	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10159351	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1025806	0.86[EUR][1000 genomes]
rs1048351	0.86[EUR][1000 genomes]
rs1048380	0.89[EUR][1000 genomes]
rs1075982	0.82[EUR][1000 genomes]
rs10789492	0.91[EUR][1000 genomes]
rs10789493	0.91[EUR][1000 genomes]
rs10890411	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10890415	0.89[EUR][1000 genomes]
rs10890416	0.89[EUR][1000 genomes]
rs11211338	0.85[EUR][1000 genomes]
rs11211341	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11211344	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11211346	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11211349	0.89[EUR][1000 genomes]
rs11211354	0.89[EUR][1000 genomes]
rs1139758	0.83[EUR][1000 genomes]
rs1150064	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1150068	0.87[EUR][1000 genomes]
rs11801316	0.85[EUR][1000 genomes]
rs11801419	0.82[EUR][1000 genomes]
rs11804665	0.83[EUR][1000 genomes]
rs12047537	0.82[EUR][1000 genomes]
rs12078635	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12082387	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12094663	0.89[EUR][1000 genomes]
rs1258052	0.87[EUR][1000 genomes]
rs1258053	0.86[EUR][1000 genomes]
rs1258054	0.87[EUR][1000 genomes]
rs1258056	0.87[EUR][1000 genomes]
rs1258059	0.87[EUR][1000 genomes]
rs13417	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1440486	0.86[EUR][1000 genomes]
rs1440489	0.86[EUR][1000 genomes]
rs1440491	0.89[EUR][1000 genomes]
rs1595898	0.82[ASN][1000 genomes]
rs17102352	0.83[EUR][1000 genomes]
rs17102355	0.83[EUR][1000 genomes]
rs17102473	0.89[EUR][1000 genomes]
rs1745377	0.87[EUR][1000 genomes]
rs1933933	0.82[EUR][1000 genomes]
rs1962900	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1971518	0.86[EUR][1000 genomes]
rs1971519	0.89[EUR][1000 genomes]
rs2083486	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2099766	0.82[ASN][1000 genomes]
rs2119301	0.86[EUR][1000 genomes]
rs2218189	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2241862	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2289446	0.82[EUR][1000 genomes]
rs2304745	0.86[EUR][1000 genomes]
rs2405026	0.86[EUR][1000 genomes]
rs2405030	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs34932727	0.86[EUR][1000 genomes]
rs3737731	0.86[EUR][1000 genomes]
rs3766211	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3766212	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3766214	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs3766215	0.86[EUR][1000 genomes]
rs3766217	0.86[EUR][1000 genomes]
rs3766219	0.91[EUR][1000 genomes]
rs3766224	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4097354	0.82[ASN][1000 genomes]
rs4272563	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4274009	0.85[EUR][1000 genomes]
rs4301586	0.85[EUR][1000 genomes]
rs4412540	0.89[EUR][1000 genomes]
rs4443838	0.82[EUR][1000 genomes]
rs4660359	0.82[ASN][1000 genomes]
rs55914029	0.84[EUR][1000 genomes]
rs56319728	0.81[EUR][1000 genomes]
rs585257	0.84[EUR][1000 genomes]
rs594118	0.89[EUR][1000 genomes]
rs595813	0.89[EUR][1000 genomes]
rs59881815	0.82[EUR][1000 genomes]
rs60173509	0.82[EUR][1000 genomes]
rs60675294	0.86[EUR][1000 genomes]
rs611468	0.89[EUR][1000 genomes]
rs614486	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61782563	0.86[EUR][1000 genomes]
rs61782564	0.86[EUR][1000 genomes]
rs61782568	0.86[EUR][1000 genomes]
rs61782590	0.84[EUR][1000 genomes]
rs61784001	0.82[EUR][1000 genomes]
rs61784002	0.82[EUR][1000 genomes]
rs61784003	0.85[EUR][1000 genomes]
rs618554	0.87[EUR][1000 genomes]
rs620431	0.87[EUR][1000 genomes]
rs620913	0.87[EUR][1000 genomes]
rs625507	0.89[EUR][1000 genomes]
rs625590	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs637760	0.89[EUR][1000 genomes]
rs638845	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6429607	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6429608	0.93[EUR][1000 genomes]
rs6429610	0.90[EUR][1000 genomes]
rs647999	0.84[EUR][1000 genomes]
rs6666405	0.87[EUR][1000 genomes]
rs6667885	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6669393	0.83[EUR][1000 genomes]
rs6670495	0.91[EUR][1000 genomes]
rs6671005	0.86[EUR][1000 genomes]
rs6671124	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6688195	0.86[EUR][1000 genomes]
rs6690193	0.89[EUR][1000 genomes]
rs723334	0.87[EUR][1000 genomes]
rs723690	0.89[EUR][1000 genomes]
rs732539	0.85[EUR][1000 genomes]
rs7354865	0.85[EUR][1000 genomes]
rs7354894	0.88[EUR][1000 genomes]
rs7412469	0.86[EUR][1000 genomes]
rs744096	0.82[EUR][1000 genomes]
rs7519866	0.93[EUR][1000 genomes]
rs7532601	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7534179	0.89[EUR][1000 genomes]
rs7541868	0.85[EUR][1000 genomes]
rs7553243	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8851	0.81[EUR][1000 genomes]
rs946320	0.87[EUR][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	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6429609	KIAA0494	Cis_1M	lymphoblastoid	RTeQTL
rs6429609	ATPAF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47185200-47189600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:47185200-47189800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:47185600-47188000	Enhancers	Stomach Mucosa	stomach
4	chr1:47185600-47188400	Weak transcription	Psoas Muscle	Psoas
5	chr1:47185600-47190600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:47185600-47190600	Weak transcription	Brain Anterior Caudate	brain
7	chr1:47185800-47188400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:47185800-47188600	Weak transcription	Adipose Nuclei	Adipose
9	chr1:47185800-47190200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:47185800-47190200	Weak transcription	Lung	lung
11	chr1:47185800-47190200	Weak transcription	Right Ventricle	heart
12	chr1:47185800-47190200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:47185800-47190400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:47185800-47190400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:47185800-47190400	Weak transcription	Left Ventricle	heart
16	chr1:47185800-47190400	Weak transcription	HepG2	liver
17	chr1:47185800-47190600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:47185800-47190600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:47185800-47190600	Weak transcription	Brain Angular Gyrus	brain
20	chr1:47185800-47190600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:47185800-47190600	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:47185800-47190600	Weak transcription	Fetal Lung	lung
23	chr1:47185800-47190600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:47185800-47190600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:47185800-47190600	Weak transcription	Hela-S3	cervix
26	chr1:47185800-47190600	Weak transcription	HMEC	breast
27	chr1:47185800-47190600	Weak transcription	NHEK	skin
28	chr1:47185800-47190800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr1:47185800-47190800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:47185800-47194000	Weak transcription	Fetal Intestine Small	intestine
31	chr1:47185800-47194200	Weak transcription	Right Atrium	heart
32	chr1:47186000-47190600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:47186800-47188400	Enhancers	K562	blood
34	chr1:47187400-47187800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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