Variant report

Variant	rs10489541
Chromosome Location	chr1:94081609-94081610
allele	C/T
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	TCF12	chr1:94080886-94081756	A549	lung:	n/a	chr1:94081221-94081228
2	POU2F2	chr1:94081261-94081779	GM12878	blood:	n/a	chr1:94081604-94081618 chr1:94081590-94081600 chr1:94081585-94081599 chr1:94081590-94081600 chr1:94081588-94081599 chr1:94081585-94081603 chr1:94081607-94081617 chr1:94081590-94081599 chr1:94081587-94081601 chr1:94081587-94081602 chr1:94081590-94081598 chr1:94081589-94081599 chr1:94081583-94081604 chr1:94081591-94081598 chr1:94081583-94081605 chr1:94081589-94081601
3	RXRA	chr1:94080470-94081771	SK-N-SH	brain:	n/a	chr1:94081362-94081384 chr1:94081271-94081284 chr1:94081330-94081339 chr1:94081270-94081277 chr1:94081271-94081284 chr1:94081271-94081284 chr1:94080827-94080843
4	JUND	chr1:94079971-94081869	SK-N-SH	brain:	n/a	chr1:94081328-94081340 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339 chr1:94081328-94081339
5	STAT3	chr1:94081433-94081834	MCF10A-Er-Src	breast:	n/a	n/a
6	NFIC	chr1:94080425-94081829	SK-N-SH	brain:	n/a	chr1:94081232-94081260
7	TCF12	chr1:94081149-94081610	GM12878	blood:	n/a	chr1:94081221-94081228
8	FOS	chr1:94080766-94081882	MCF10A-Er-Src	breast:	n/a	chr1:94081328-94081340 chr1:94081328-94081339 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339
9	TEAD4	chr1:94080426-94081863	SK-N-SH	brain:	n/a	chr1:94080668-94080677
10	MAX	chr1:94080209-94081732	A549	lung:	n/a	chr1:94081330-94081339 chr1:94081329-94081338
11	CUX1	chr1:94081222-94081640	GM12878	blood:	n/a	n/a
12	FOS	chr1:94081161-94081951	MCF10A-Er-Src	breast:	n/a	chr1:94081328-94081340 chr1:94081328-94081339 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339
13	FOSL2	chr1:94081073-94081621	SK-N-SH	brain:	n/a	chr1:94081328-94081340 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339
14	BATF	chr1:94081220-94081703	GM12878	blood:	n/a	chr1:94081331-94081341
15	SRF	chr1:94081082-94081612	GM12878	blood:	n/a	n/a
16	SREBP1	chr1:94080401-94082190	GM12878	blood:	n/a	n/a
17	MEF2A	chr1:94081188-94082003	GM12878	blood:	n/a	chr1:94081725-94081740
18	MAX	chr1:94081027-94081709	SK-N-SH	brain:	n/a	chr1:94081330-94081339 chr1:94081329-94081338
19	SP1	chr1:94081103-94081786	A549	lung:	n/a	chr1:94081467-94081478
20	RUNX3	chr1:94080681-94081906	GM12878	blood:	n/a	n/a
21	MAFK	chr1:94081477-94081646	IMR90	lung:	n/a	n/a
22	POU2F2	chr1:94081293-94081745	GM12878	blood:	n/a	chr1:94081604-94081618 chr1:94081590-94081600 chr1:94081585-94081599 chr1:94081590-94081600 chr1:94081588-94081599 chr1:94081585-94081603 chr1:94081607-94081617 chr1:94081590-94081599 chr1:94081587-94081601 chr1:94081587-94081602 chr1:94081590-94081598 chr1:94081589-94081599 chr1:94081583-94081604 chr1:94081591-94081598 chr1:94081583-94081605 chr1:94081589-94081601
23	FOSL2	chr1:94080393-94081846	SK-N-SH	brain:	n/a	chr1:94081328-94081340 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339
24	FOS	chr1:94080138-94081878	MCF10A-Er-Src	breast:	n/a	chr1:94081328-94081340 chr1:94081328-94081339 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339
25	STAT3	chr1:94081429-94081834	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr1:94080678-94081737	GM12892	blood:	n/a	n/a
27	MXI1	chr1:94078695-94084544	SK-N-SH	brain:	n/a	chr1:94082665-94082680
28	FOSL2	chr1:94080585-94081635	HepG2	liver:	n/a	chr1:94081328-94081340 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339
29	MAX	chr1:94080525-94081620	HepG2	liver:	n/a	chr1:94081330-94081339 chr1:94081329-94081338
30	STAT5A	chr1:94080943-94081791	GM12878	blood:	n/a	chr1:94081330-94081339 chr1:94081329-94081338 chr1:94081010-94081017 chr1:94081025-94081033
31	BCLAF1	chr1:94080690-94081833	GM12878	blood:	n/a	chr1:94081329-94081338 chr1:94081330-94081339
32	ATF2	chr1:94081250-94081834	GM12878	blood:	n/a	n/a
33	JUND	chr1:94080456-94081813	SK-N-SH	brain:	n/a	chr1:94081328-94081340 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339 chr1:94081328-94081339
34	BACH1	chr1:94081071-94081782	H1-hESC	embryonic stem cell:	n/a	chr1:94081327-94081341
35	TBL1XR1	chr1:94080814-94082104	GM12878	blood:	n/a	n/a
36	BATF	chr1:94080801-94081729	GM12878	blood:	n/a	chr1:94081331-94081341
37	RELA	chr1:94080860-94081774	GM19193	blood:	n/a	n/a
38	POU2F2	chr1:94080745-94081745	GM12891	blood:	n/a	chr1:94081604-94081618 chr1:94081590-94081600 chr1:94081585-94081599 chr1:94081590-94081600 chr1:94081588-94081599 chr1:94081585-94081603 chr1:94081607-94081617 chr1:94081590-94081599 chr1:94081587-94081601 chr1:94081587-94081602 chr1:94081590-94081598 chr1:94081589-94081599 chr1:94081583-94081604 chr1:94081591-94081598 chr1:94081583-94081605 chr1:94081589-94081601
39	IRF4	chr1:94081081-94081775	GM12878	blood:	n/a	n/a
40	TCF12	chr1:94081274-94081637	GM12878	blood:	n/a	n/a
41	EBF1	chr1:94081220-94081871	GM12878	blood:	n/a	n/a
42	FOS	chr1:94081184-94082153	MCF10A-Er-Src	breast:	n/a	chr1:94081328-94081340 chr1:94081328-94081339 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339
43	MTA3	chr1:94081180-94081728	GM12878	blood:	n/a	n/a
44	CEBPB	chr1:94081379-94081758	GM12878	blood:	n/a	n/a
45	EP300	chr1:94080733-94081862	GM12878	blood:	n/a	chr1:94081330-94081339
46	PAX5	chr1:94080733-94081750	GM12878	blood:	n/a	n/a
47	NFIC	chr1:94080653-94082013	GM12878	blood:	n/a	chr1:94081232-94081260
48	BCL11A	chr1:94080728-94081710	GM12878	blood:	n/a	chr1:94081329-94081338 chr1:94081330-94081339
49	JUND	chr1:94080462-94081817	SK-N-SH	brain:	n/a	chr1:94081328-94081340 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339 chr1:94081328-94081339
50	PBX3	chr1:94081130-94081635	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:94048472..94052407-chr1:94077212..94082015,4	MCF-7	breast:
2	chr1:94079454..94081293-chr1:94081521..94084323,2	K562	blood:
3	chr1:94074700..94077458-chr1:94080437..94082607,3	K562	blood:
4	chr1:94079843..94082142-chr1:94311555..94313576,2	K562	blood:
5	chr1:94070552..94073246-chr1:94081177..94083185,2	MCF-7	breast:
6	chr1:94080816..94083593-chr1:94090826..94092537,2	K562	blood:
7	chr1:93903600..93904188-chr1:94081046..94081681,2	K562	blood:

Variant related genes	Relation type
BCAR3	TF binding region
ENSG00000137936	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000211575	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11164954	1.00[EUR][1000 genomes]
rs11800247	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11802499	1.00[EUR][1000 genomes]
rs11805042	1.00[EUR][1000 genomes]
rs11806965	1.00[EUR][1000 genomes]
rs1593513	1.00[EUR][1000 genomes]
rs1593514	1.00[EUR][1000 genomes]
rs1593515	1.00[EUR][1000 genomes]
rs17110193	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17110312	1.00[EUR][1000 genomes]
rs17110320	1.00[EUR][1000 genomes]
rs2221923	1.00[EUR][1000 genomes]
rs236309	1.00[EUR][1000 genomes]
rs4475764	1.00[EUR][1000 genomes]
rs57453256	1.00[EUR][1000 genomes]
rs58024738	1.00[EUR][1000 genomes]
rs58591926	1.00[EUR][1000 genomes]
rs58679238	1.00[EUR][1000 genomes]
rs59653321	1.00[EUR][1000 genomes]
rs60188127	1.00[EUR][1000 genomes]
rs61372707	1.00[EUR][1000 genomes]
rs61658240	0.87[AMR][1000 genomes]
rs6541391	1.00[EUR][1000 genomes]
rs6541392	1.00[EUR][1000 genomes]
rs6657187	1.00[EUR][1000 genomes]
rs6661879	1.00[EUR][1000 genomes]
rs6671646	1.00[EUR][1000 genomes]
rs6686775	1.00[EUR][1000 genomes]
rs72963382	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7525976	1.00[EUR][1000 genomes]
rs871855	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94057600-94106400	Weak transcription	Primary B cells from cord blood	blood
2	chr1:94077200-94099000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:94077600-94084200	Enhancers	Fetal Brain Male	brain
4	chr1:94078400-94084200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr1:94078600-94084400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:94078800-94084200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr1:94078800-94084200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:94079000-94084000	Enhancers	Brain Substantia Nigra	brain
9	chr1:94079200-94081800	Enhancers	Placenta Amnion	Placenta Amnion
10	chr1:94079200-94082800	Enhancers	Duodenum Mucosa	Duodenum
11	chr1:94079200-94084000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr1:94079200-94084000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:94079200-94084200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr1:94079400-94083400	Enhancers	Esophagus	oesophagus
15	chr1:94079400-94084000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:94079400-94084200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:94079400-94084800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:94079400-94086800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:94079400-94088600	Enhancers	Fetal Intestine Large	intestine
20	chr1:94079600-94082200	Enhancers	Brain Germinal Matrix	brain
21	chr1:94079600-94082600	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr1:94079600-94084200	Enhancers	Fetal Brain Female	brain
23	chr1:94079600-94088000	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr1:94079600-94089400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:94079800-94081800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr1:94079800-94082400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:94079800-94082800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:94079800-94082800	Enhancers	Liver	Liver
29	chr1:94079800-94084000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:94079800-94084000	Enhancers	Fetal Muscle Trunk	muscle
31	chr1:94079800-94084000	Enhancers	Left Ventricle	heart
32	chr1:94079800-94084200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:94079800-94084200	Enhancers	Placenta	Placenta
34	chr1:94079800-94084600	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr1:94079800-94090000	Enhancers	Stomach Mucosa	stomach
36	chr1:94080000-94083800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:94080000-94084000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:94080000-94084000	Enhancers	Right Atrium	heart
39	chr1:94080000-94084200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:94080000-94084200	Enhancers	Fetal Muscle Leg	muscle
41	chr1:94080000-94088000	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr1:94080000-94089200	Genic enhancers	NHEK	skin
43	chr1:94080200-94082200	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:94080200-94082400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:94080200-94083400	Enhancers	Adipose Nuclei	Adipose
46	chr1:94080200-94084400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:94080400-94081800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:94080400-94082000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:94080400-94082200	Weak transcription	Brain Angular Gyrus	brain
50	chr1:94080400-94082600	Weak transcription	Fetal Lung	lung

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