Variant report

Variant	rs236306
Chromosome Location	chr1:94081407-94081408
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	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	MAFK	chr1:94080693-94081492	HepG2	liver:	n/a	chr1:94081331-94081340 chr1:94081329-94081344 chr1:94081330-94081340
5	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
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	CHD2	chr1:94081208-94081596	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr1:94081143-94081504	HCT-116	colon:	n/a	n/a
15	FOSL2	chr1:94081073-94081621	SK-N-SH	brain:	n/a	chr1:94081328-94081340 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339
16	EBF1	chr1:94080732-94081538	GM12878	blood:	n/a	n/a
17	BATF	chr1:94081220-94081703	GM12878	blood:	n/a	chr1:94081331-94081341
18	SRF	chr1:94081082-94081612	GM12878	blood:	n/a	n/a
19	SREBP1	chr1:94080401-94082190	GM12878	blood:	n/a	n/a
20	MEF2A	chr1:94081188-94082003	GM12878	blood:	n/a	chr1:94081725-94081740
21	REST	chr1:94081298-94081596	SK-N-SH	brain:	n/a	n/a
22	YY1	chr1:94081213-94081484	HCT-116	colon:	n/a	n/a
23	MAX	chr1:94081027-94081709	SK-N-SH	brain:	n/a	chr1:94081330-94081339 chr1:94081329-94081338
24	SMC3	chr1:94081352-94081552	GM12878	blood:	n/a	n/a
25	SP1	chr1:94081103-94081786	A549	lung:	n/a	chr1:94081467-94081478
26	RUNX3	chr1:94080681-94081906	GM12878	blood:	n/a	n/a
27	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
28	FOSL2	chr1:94080393-94081846	SK-N-SH	brain:	n/a	chr1:94081328-94081340 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339
29	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
30	STAT3	chr1:94081318-94081449	MCF10A-Er-Src	breast:	n/a	chr1:94081330-94081339 chr1:94081329-94081338
31	WRNIP1	chr1:94081398-94081598	GM12878	blood:	n/a	n/a
32	JUND	chr1:94081116-94081598	HepG2	liver:	n/a	chr1:94081328-94081340 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339 chr1:94081328-94081339
33	POLR2A	chr1:94080678-94081737	GM12892	blood:	n/a	n/a
34	TCF7L2	chr1:94081159-94081444	HCT-116	colon:	n/a	chr1:94081269-94081285 chr1:94081269-94081285 chr1:94081330-94081339 chr1:94081274-94081281 chr1:94081273-94081282 chr1:94081270-94081284 chr1:94081271-94081281 chr1:94081272-94081281
35	JUND	chr1:94081210-94081557	A549	lung:	n/a	chr1:94081328-94081340 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339 chr1:94081328-94081339
36	JUN	chr1:94081162-94081453	H1-hESC	embryonic stem cell:	n/a	chr1:94081328-94081340 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339
37	MXI1	chr1:94078695-94084544	SK-N-SH	brain:	n/a	chr1:94082665-94082680
38	CHD2	chr1:94081212-94081412	HepG2	liver:	n/a	n/a
39	FOSL2	chr1:94080585-94081635	HepG2	liver:	n/a	chr1:94081328-94081340 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339
40	MAX	chr1:94080525-94081620	HepG2	liver:	n/a	chr1:94081330-94081339 chr1:94081329-94081338
41	FOSL2	chr1:94080591-94081564	HepG2	liver:	n/a	chr1:94081328-94081340 chr1:94081330-94081337 chr1:94081330-94081338 chr1:94081330-94081339
42	TEAD4	chr1:94080503-94081536	HepG2	liver:	n/a	chr1:94080668-94080677
43	STAT5A	chr1:94080943-94081791	GM12878	blood:	n/a	chr1:94081330-94081339 chr1:94081329-94081338 chr1:94081010-94081017 chr1:94081025-94081033
44	BCLAF1	chr1:94080690-94081833	GM12878	blood:	n/a	chr1:94081329-94081338 chr1:94081330-94081339
45	TCF7L2	chr1:94081030-94081518	PANC-1	pancreas:	n/a	chr1:94081269-94081285 chr1:94081269-94081285 chr1:94081330-94081339 chr1:94081274-94081281 chr1:94081273-94081282 chr1:94081270-94081284 chr1:94081271-94081281 chr1:94081272-94081281
46	MBD4	chr1:94080689-94081463	HepG2	liver:	n/a	n/a
47	ATF2	chr1:94081250-94081834	GM12878	blood:	n/a	n/a
48	MAFF	chr1:94081184-94081481	K562	blood:	n/a	chr1:94081328-94081346
49	MBD4	chr1:94080691-94081485	HepG2	liver:	n/a	n/a
50	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

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

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

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1772781	0.81[ASN][1000 genomes]
rs1772782	0.81[ASN][1000 genomes]
rs236273	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs236288	0.82[AMR][1000 genomes]
rs236291	0.87[AMR][1000 genomes]
rs236301	0.85[AMR][1000 genomes]
rs236307	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs236308	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236311	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236312	1.00[CEU][hapmap];0.84[CHD][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs236313	0.84[CHD][hapmap]
rs236343	0.82[CEU][hapmap];0.86[CHB][hapmap];0.91[AMR][1000 genomes]
rs236344	0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.80[LWK][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs236345	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs368888	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3767979	0.86[CHB][hapmap]
rs399649	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs423493	1.00[CEU][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798213	0.85[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs798217	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798218	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs236306	BCAR3	cis	parietal	SCAN

Chromatin state (count:114 , 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	chr1:94079400-94081600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:94079400-94083400	Enhancers	Esophagus	oesophagus
16	chr1:94079400-94084000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:94079400-94084200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:94079400-94084800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:94079400-94086800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:94079400-94088600	Enhancers	Fetal Intestine Large	intestine
21	chr1:94079600-94081600	Enhancers	Colonic Mucosa	Colon
22	chr1:94079600-94082200	Enhancers	Brain Germinal Matrix	brain
23	chr1:94079600-94082600	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr1:94079600-94084200	Enhancers	Fetal Brain Female	brain
25	chr1:94079600-94088000	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr1:94079600-94089400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:94079800-94081800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr1:94079800-94082400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:94079800-94082800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:94079800-94082800	Enhancers	Liver	Liver
31	chr1:94079800-94084000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:94079800-94084000	Enhancers	Fetal Muscle Trunk	muscle
33	chr1:94079800-94084000	Enhancers	Left Ventricle	heart
34	chr1:94079800-94084200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:94079800-94084200	Enhancers	Placenta	Placenta
36	chr1:94079800-94084600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr1:94079800-94090000	Enhancers	Stomach Mucosa	stomach
38	chr1:94080000-94081600	Enhancers	Psoas Muscle	Psoas
39	chr1:94080000-94083800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:94080000-94084000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:94080000-94084000	Enhancers	Right Atrium	heart
42	chr1:94080000-94084200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:94080000-94084200	Enhancers	Fetal Muscle Leg	muscle
44	chr1:94080000-94088000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr1:94080000-94089200	Genic enhancers	NHEK	skin
46	chr1:94080200-94082200	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:94080200-94082400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:94080200-94083400	Enhancers	Adipose Nuclei	Adipose
49	chr1:94080200-94084400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:94080400-94081600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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