Variant report

Variant	rs236307
Chromosome Location	chr1:94082917-94082918
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	TBP	chr1:94082643-94084091	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:94082613-94083470	Hela-S3	cervix:	n/a	n/a
3	HEY1	chr1:94082661-94084077	HepG2	liver:	n/a	n/a
4	MBD4	chr1:94082628-94084144	HepG2	liver:	n/a	n/a
5	HDAC2	chr1:94082844-94083631	HepG2	liver:	n/a	chr1:94083399-94083418 chr1:94083340-94083348
6	NFIC	chr1:94082633-94084145	HepG2	liver:	n/a	n/a
7	ARID3A	chr1:94082858-94084357	HepG2	liver:	n/a	n/a
8	MAFK	chr1:94082760-94084074	HepG2	liver:	n/a	chr1:94083350-94083365
9	EP300	chr1:94082756-94084220	HepG2	liver:	n/a	chr1:94083281-94083295
10	POLR2A	chr1:94082092-94084387	HepG2	liver:	n/a	n/a
11	FOS	chr1:94082750-94083197	HUVEC	blood vessel:	n/a	chr1:94083048-94083057 chr1:94083046-94083057
12	RFX5	chr1:94082528-94084054	HepG2	liver:	n/a	chr1:94082663-94082680 chr1:94082664-94082679 chr1:94082664-94082679 chr1:94082664-94082679
13	MXI1	chr1:94078695-94084544	SK-N-SH	brain:	n/a	chr1:94082665-94082680
14	JUN	chr1:94082883-94083467	HepG2	liver:	n/a	chr1:94083048-94083057 chr1:94083281-94083294
15	MAZ	chr1:94082796-94083977	HepG2	liver:	n/a	chr1:94083284-94083293
16	POLR2A	chr1:94082647-94083095	A549	lung:	n/a	n/a
17	POLR2A	chr1:94082666-94083022	HepG2	liver:	n/a	n/a
18	FOXA2	chr1:94082895-94084066	HepG2	liver:	n/a	n/a
19	MAX	chr1:94082469-94084187	HepG2	liver:	n/a	chr1:94082705-94082715 chr1:94082669-94082678 chr1:94083284-94083293
20	POLR2A	chr1:94082604-94084384	HepG2	liver:	n/a	n/a
21	HEY1	chr1:94082465-94084268	HepG2	liver:	n/a	n/a
22	MAX	chr1:94082520-94083809	A549	lung:	n/a	chr1:94082669-94082678 chr1:94082705-94082715 chr1:94083284-94083293
23	JUND	chr1:94082820-94083659	HepG2	liver:	n/a	chr1:94083048-94083057 chr1:94083046-94083057
24	MBD4	chr1:94082765-94084178	HepG2	liver:	n/a	n/a
25	EP300	chr1:94082527-94084080	HepG2	liver:	n/a	chr1:94083281-94083295
26	FOSL2	chr1:94082759-94083353	HepG2	liver:	n/a	chr1:94083048-94083057 chr1:94083047-94083058
27	RCOR1	chr1:94082884-94084086	HepG2	liver:	n/a	n/a
28	SP1	chr1:94082697-94084226	HepG2	liver:	n/a	chr1:94083450-94083457
29	MXI1	chr1:94082579-94084102	HepG2	liver:	n/a	chr1:94082665-94082680
30	JUND	chr1:94082912-94083437	HepG2	liver:	n/a	chr1:94083048-94083057 chr1:94083046-94083057
31	EP300	chr1:94082872-94084137	HepG2	liver:	n/a	chr1:94083281-94083295
32	MAX	chr1:94082640-94084019	HepG2	liver:	n/a	chr1:94082705-94082715 chr1:94082669-94082678 chr1:94083284-94083293
33	POLR2A	chr1:94082068-94083938	Hela-S3	cervix:	n/a	n/a
34	BHLHE40	chr1:94082843-94084049	HepG2	liver:	n/a	n/a
35	TCF12	chr1:94082447-94083751	A549	lung:	n/a	chr1:94083308-94083318
36	SP1	chr1:94082836-94083629	A549	lung:	n/a	chr1:94083450-94083457
37	NFIC	chr1:94082745-94084265	HepG2	liver:	n/a	n/a
38	MAX	chr1:94082797-94083646	A549	lung:	n/a	chr1:94083284-94083293
39	POLR2A	chr1:94082421-94084211	HepG2	liver:	n/a	n/a
40	POLR2A	chr1:94082666-94084061	HepG2	liver:	n/a	n/a
41	POLR2A	chr1:94082904-94083549	HepG2	liver:	n/a	n/a
42	HNF4A	chr1:94082665-94084093	HepG2	liver:	n/a	chr1:94083339-94083354 chr1:94083341-94083353 chr1:94082760-94082775 chr1:94083341-94083353 chr1:94083339-94083354 chr1:94083339-94083354 chr1:94083341-94083353 chr1:94083338-94083356 chr1:94083339-94083354 chr1:94083340-94083353
43	MYC	chr1:94082587-94083077	MCF10A-Er-Src	breast:	n/a	chr1:94082705-94082715 chr1:94082669-94082678
44	FOSL2	chr1:94082372-94083438	A549	lung:	n/a	chr1:94083048-94083057 chr1:94083047-94083058
45	JUND	chr1:94082775-94084009	HepG2	liver:	n/a	chr1:94083048-94083057 chr1:94083046-94083057
46	USF2	chr1:94082763-94083106	HepG2	liver:	n/a	n/a
47	TEAD4	chr1:94082768-94084249	HepG2	liver:	n/a	n/a
48	GATA2	chr1:94081982-94083052	SH-SY5Y	brain:	n/a	n/a
49	MAFK	chr1:94082800-94084131	HepG2	liver:	n/a	chr1:94083350-94083365
50	POLR2A	chr1:94082093-94083958	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:94079454..94081293-chr1:94081521..94084323,2	K562	blood:
2	chr1:94070552..94073246-chr1:94081177..94083185,2	MCF-7	breast:
3	chr1:94080816..94083593-chr1:94090826..94092537,2	K562	blood:

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

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12568405	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1772781	0.88[CHB][hapmap]
rs236273	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs236288	0.81[AMR][1000 genomes]
rs236291	0.85[AMR][1000 genomes]
rs236301	0.84[AMR][1000 genomes]
rs236306	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];0.88[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs236311	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs236312	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs236313	0.88[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs236343	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes]
rs236344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs236345	0.85[EUR][1000 genomes]
rs368888	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3767979	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs399649	0.88[CHB][hapmap];0.84[CHD][hapmap]
rs423493	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs798213	0.85[CEU][hapmap];0.88[CHB][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs798217	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs798218	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs932523	0.86[ASW][hapmap]

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
rs236307	BCAR3	cis	parietal	SCAN

Chromatin state (count:106 , 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	chr1:94079200-94084000	Enhancers	H1 Cell Line	embryonic stem cell
10	chr1:94079200-94084000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:94079200-94084200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr1:94079400-94083400	Enhancers	Esophagus	oesophagus
13	chr1:94079400-94084000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:94079400-94084200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:94079400-94084800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:94079400-94086800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:94079400-94088600	Enhancers	Fetal Intestine Large	intestine
18	chr1:94079600-94084200	Enhancers	Fetal Brain Female	brain
19	chr1:94079600-94088000	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr1:94079600-94089400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:94079800-94084000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:94079800-94084000	Enhancers	Fetal Muscle Trunk	muscle
23	chr1:94079800-94084000	Enhancers	Left Ventricle	heart
24	chr1:94079800-94084200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:94079800-94084200	Enhancers	Placenta	Placenta
26	chr1:94079800-94084600	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr1:94079800-94090000	Enhancers	Stomach Mucosa	stomach
28	chr1:94080000-94083800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:94080000-94084000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:94080000-94084000	Enhancers	Right Atrium	heart
31	chr1:94080000-94084200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:94080000-94084200	Enhancers	Fetal Muscle Leg	muscle
33	chr1:94080000-94088000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr1:94080000-94089200	Genic enhancers	NHEK	skin
35	chr1:94080200-94083400	Enhancers	Adipose Nuclei	Adipose
36	chr1:94080200-94084400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:94080400-94083200	Enhancers	HMEC	breast
38	chr1:94080400-94084000	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr1:94080600-94083400	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr1:94080600-94084400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:94080600-94084800	Enhancers	Primary B cells from peripheral blood	blood
42	chr1:94080800-94084200	Enhancers	HUVEC	blood vessel
43	chr1:94080800-94084400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:94081000-94084000	Enhancers	Spleen	Spleen
45	chr1:94081000-94084000	Enhancers	NHDF-Ad	bronchial
46	chr1:94081000-94084200	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr1:94081200-94083800	Enhancers	NHLF	lung
48	chr1:94081200-94084200	Flanking Active TSS	A549	lung
49	chr1:94081200-94084400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:94081200-94084600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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