Variant report

Variant	rs4268459
Chromosome Location	chr10:52383271-52383272
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	ZBTB7A	chr10:52382916-52383344	HepG2	liver:	n/a	n/a
2	ELF1	chr10:52382439-52385283	GM12878	blood:	n/a	chr10:52385128-52385140 chr10:52384980-52384989
3	TCF12	chr10:52383264-52383590	GM12878	blood:	n/a	n/a
4	POLR2A	chr10:52381694-52385975	Hela-S3	cervix:	n/a	n/a
5	EGR1	chr10:52382920-52383575	K562	blood:	n/a	chr10:52383220-52383234 chr10:52383506-52383519 chr10:52383342-52383355 chr10:52383341-52383356 chr10:52383342-52383355
6	MXI1	chr10:52381308-52386209	SK-N-SH	brain:	n/a	chr10:52384448-52384457 chr10:52384446-52384455
7	POLR2A	chr10:52383148-52385231	A549	lung:	n/a	n/a
8	POLR2A	chr10:52383216-52385848	GM12892	blood:	n/a	n/a
9	MAX	chr10:52382912-52385590	A549	lung:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52384445-52384454
10	MAZ	chr10:52382568-52385628	Hela-S3	cervix:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52384445-52384454
11	HDAC2	chr10:52382948-52383969	MCF-7	breast:	n/a	n/a
12	ZEB1	chr10:52383123-52383942	GM12878	blood:	n/a	n/a
13	RELA	chr10:52382955-52385813	GM15510	blood:	n/a	n/a
14	MXI1	chr10:52383092-52385294	HepG2	liver:	n/a	chr10:52384448-52384457 chr10:52384446-52384455
15	JUN	chr10:52383103-52385367	K562	blood:	n/a	chr10:52384395-52384409 chr10:52384342-52384351 chr10:52384347-52384356
16	RCOR1	chr10:52383170-52385942	K562	blood:	n/a	n/a
17	POLR2A	chr10:52382059-52385792	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr10:52383010-52385273	MCF-7	breast:	n/a	n/a
19	CTBP2	chr10:52383180-52385115	H1-hESC	embryonic stem cell:	n/a	n/a
20	ETS1	chr10:52383132-52383748	K562	blood:	n/a	chr10:52383280-52383293
21	ETS1	chr10:52383209-52384095	K562	blood:	n/a	chr10:52383280-52383293
22	EP300	chr10:52383153-52385414	SK-N-SH	brain:	n/a	chr10:52383649-52383665 chr10:52383417-52383426 chr10:52384373-52384389 chr10:52383648-52383664 chr10:52383733-52383749 chr10:52384377-52384393 chr10:52384821-52384837 chr10:52383652-52383668
23	POLR2A	chr10:52382463-52385929	K562	blood:	n/a	n/a
24	ZBTB7A	chr10:52382515-52384180	K562	blood:	n/a	n/a
25	POLR2A	chr10:52381492-52385682	GM12878	blood:	n/a	n/a
26	MAX	chr10:52382428-52385706	K562	blood:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52384445-52384454 chr10:52382485-52382494
27	MYC	chr10:52381671-52385865	K562	blood:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52382022-52382032 chr10:52384445-52384454 chr10:52382485-52382494
28	EGR1	chr10:52383134-52383424	GM12878	blood:	n/a	chr10:52383220-52383234 chr10:52383342-52383355 chr10:52383341-52383356 chr10:52383342-52383355
29	CREB1	chr10:52383230-52385187	K562	blood:	n/a	n/a
30	POLR2A	chr10:52381565-52385941	PBDE	blood:	n/a	n/a
31	POLR2A	chr10:52383043-52385337	ECC-1	luminal epithelium:	n/a	n/a
32	CREB1	chr10:52383197-52385429	GM12878	blood:	n/a	n/a
33	POLR2A	chr10:52382987-52385916	GM12891	blood:	n/a	n/a
34	POLR2A	chr10:52383231-52385369	H1-neurons	neurons:	n/a	n/a
35	CCNT2	chr10:52382519-52385293	K562	blood:	n/a	chr10:52384626-52384635
36	ZKSCAN1	chr10:52383251-52383440	Hela-S3	cervix:	n/a	n/a
37	MAX	chr10:52383125-52385873	NB4	blood:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52384445-52384454
38	SIN3AK20	chr10:52382799-52385142	PANC-1	pancreas:	n/a	n/a
39	POLR2A	chr10:52383265-52385764	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr10:52382701-52385868	NB4	blood:	n/a	n/a
41	POLR2A	chr10:52383012-52385617	GM12892	blood:	n/a	n/a
42	MAX	chr10:52383149-52384793	K562	blood:	n/a	chr10:52384447-52384456 chr10:52384446-52384456 chr10:52384445-52384454
43	POLR2A	chr10:52383163-52383333	ProgFib	skin:	n/a	n/a
44	POLR2A	chr10:52381663-52385862	K562	blood:	n/a	n/a
45	POLR2A	chr10:52381579-52385837	Hela-S3	cervix:	n/a	n/a
46	TAF1	chr10:52382999-52384087	K562	blood:	n/a	n/a
47	TFAP2C	chr10:52381634-52385658	Hela-S3	cervix:	n/a	chr10:52385338-52385353 chr10:52384461-52384476
48	ZBTB7A	chr10:52382521-52383530	K562	blood:	n/a	n/a
49	RELA	chr10:52383046-52385824	GM10847	blood:	n/a	n/a
50	POLR2A	chr10:52383256-52383948	Gliobla	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:52343575..52346402-chr10:52381237..52383627,2	K562	blood:
2	chr10:52173595..52180106-chr10:52381535..52385847,7	MCF-7	breast:
3	chr10:52342227..52348125-chr10:52381237..52386507,8	K562	blood:
4	chr10:52383202..52384098-chr16:67280868..67281485,2	Hela-S3	cervix:
5	chr10:52229715..52232627-chr10:52381775..52384727,3	MCF-7	breast:
6	chr10:52341787..52346100-chr10:52382899..52385718,8	MCF-7	breast:
7	chr10:52176732..52178529-chr10:52382760..52384432,2	MCF-7	breast:
8	chr10:52381243..52386496-chr10:52418227..52421959,6	MCF-7	breast:
9	chr10:52382538..52386733-chr10:52497918..52501112,4	MCF-7	breast:
10	chr10:52358660..52367648-chr10:52378481..52386533,25	MCF-7	breast:
11	chr10:52365691..52371767-chr10:52381261..52385919,7	K562	blood:
12	chr10:52173619..52179913-chr10:52381938..52386991,6	K562	blood:
13	chr10:52229968..52233210-chr10:52382214..52385931,3	MCF-7	breast:
14	chr10:52356810..52366659-chr10:52378806..52385975,25	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226200	TF binding region
ENSG00000198964	Chromatin interaction
ENSG00000251950	Chromatin interaction
ENSG00000225303	Chromatin interaction
ENSG00000204147	Chromatin interaction
ENSG00000230036	Chromatin interaction
ENSG00000231345	Chromatin interaction
ENSG00000135723	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10740762	0.94[EUR][1000 genomes]
rs10763590	0.93[EUR][1000 genomes]
rs10826242	0.94[EUR][1000 genomes]
rs11006281	0.97[ASN][1000 genomes]
rs17497064	0.94[ASN][1000 genomes]
rs3001879	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3001883	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3001885	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3011714	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4935735	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4935736	0.94[EUR][1000 genomes]
rs4935737	0.94[ASN][1000 genomes]
rs4935739	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6481442	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6481461	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7067552	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7073182	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7089882	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7090996	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7094655	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7097359	0.94[EUR][1000 genomes]
rs7903649	0.94[EUR][1000 genomes]
rs7904101	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908136	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7909486	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7918559	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[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	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking 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 target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS 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	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4268459	FLJ31958	N/A	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52380800-52385400	Active TSS	Rectal Smooth Muscle	rectum
2	chr10:52381200-52384200	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr10:52381200-52386000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr10:52381400-52383400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr10:52381400-52384400	Active TSS	Right Atrium	heart
6	chr10:52381400-52385400	Active TSS	Brain Cingulate Gyrus	brain
7	chr10:52381400-52385800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr10:52381400-52386000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr10:52381400-52386200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr10:52381600-52385200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr10:52381600-52385200	Active TSS	Primary T killer memory cells from peripheral blood	blood
12	chr10:52381600-52385200	Active TSS	Brain Hippocampus Middle	brain
13	chr10:52381600-52385400	Active TSS	Psoas Muscle	Psoas
14	chr10:52381600-52385600	Active TSS	Colon Smooth Muscle	Colon
15	chr10:52381600-52385600	Active TSS	Left Ventricle	heart
16	chr10:52381600-52385600	Active TSS	Ovary	ovary
17	chr10:52381600-52385800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr10:52381600-52385800	Active TSS	H9 Cell Line	embryonic stem cell
19	chr10:52381600-52385800	Active TSS	Fetal Heart	heart
20	chr10:52381800-52385200	Active TSS	Primary T cells from cord blood	blood
21	chr10:52381800-52385400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr10:52381800-52385400	Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr10:52381800-52385400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr10:52381800-52385400	Active TSS	Brain Angular Gyrus	brain
25	chr10:52381800-52385400	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr10:52381800-52385400	Active TSS	Brain Substantia Nigra	brain
27	chr10:52381800-52385400	Active TSS	Fetal Intestine Small	intestine
28	chr10:52381800-52385400	Active TSS	Fetal Kidney	kidney
29	chr10:52381800-52385400	Active TSS	Lung	lung
30	chr10:52381800-52385400	Active TSS	Small Intestine	intestine
31	chr10:52381800-52385400	Active TSS	Spleen	Spleen
32	chr10:52381800-52385400	Active TSS	GM12878-XiMat	blood
33	chr10:52381800-52385400	Active TSS	HSMMtube	muscle
34	chr10:52381800-52385600	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr10:52381800-52385600	Active TSS	Gastric	stomach
36	chr10:52381800-52385600	Active TSS	Pancreas	Pancrea
37	chr10:52381800-52385600	Active TSS	Right Ventricle	heart
38	chr10:52381800-52385600	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr10:52381800-52385800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:52381800-52385800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr10:52381800-52385800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr10:52381800-52385800	Active TSS	A549	lung
43	chr10:52381800-52386000	Active TSS	Fetal Intestine Large	intestine
44	chr10:52382000-52383600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr10:52382000-52383600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr10:52382000-52384200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr10:52382000-52385200	Active TSS	Liver	Liver
48	chr10:52382000-52385200	Active TSS	Brain Anterior Caudate	brain
49	chr10:52382000-52385200	Active TSS	Thymus	Thymus
50	chr10:52382000-52385600	Active TSS	Aorta	Aorta

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