Variant report

Variant	rs6736664
Chromosome Location	chr2:10857763-10857764
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	SIN3AK20	chr2:10857740-10858056	SK-N-SH	brain:	n/a	n/a
2	STAT3	chr2:10857607-10858169	MCF10A-Er-Src	breast:	n/a	n/a
3	PBX3	chr2:10857586-10858263	SK-N-SH	brain:	n/a	n/a
4	TBP	chr2:10857525-10858016	Hela-S3	cervix:	n/a	n/a
5	FOS	chr2:10857746-10858182	MCF10A-Er-Src	breast:	n/a	n/a
6	RAD21	chr2:10857753-10858044	Hela-S3	cervix:	n/a	n/a
7	FOS	chr2:10857656-10858245	MCF10A-Er-Src	breast:	n/a	n/a
8	TCF7L2	chr2:10857759-10858075	Hela-S3	cervix:	n/a	n/a
9	NFIC	chr2:10857648-10858251	SK-N-SH	brain:	n/a	n/a
10	MYC	chr2:10857672-10858085	MCF10A-Er-Src	breast:	n/a	chr2:10857713-10857724
11	FOS	chr2:10857634-10858182	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr2:10857690-10858195	SK-N-SH	brain:	n/a	n/a
13	STAT3	chr2:10857731-10858147	Hela-S3	cervix:	n/a	n/a
14	STAT3	chr2:10857708-10858256	MCF10A-Er-Src	breast:	n/a	n/a
15	NFIC	chr2:10857479-10858389	SK-N-SH	brain:	n/a	n/a
16	TEAD4	chr2:10857649-10858264	ECC-1	luminal epithelium:	n/a	n/a
17	JUND	chr2:10857651-10858338	SK-N-SH	brain:	n/a	n/a
18	GATA3	chr2:10857553-10858193	SK-N-SH	brain:	n/a	n/a
19	NFIC	chr2:10857685-10858177	ECC-1	luminal epithelium:	n/a	n/a
20	STAT3	chr2:10857539-10858228	MCF10A-Er-Src	breast:	n/a	n/a
21	JUND	chr2:10857614-10858323	SK-N-SH	brain:	n/a	n/a
22	BRCA1	chr2:10857737-10858035	Hela-S3	cervix:	n/a	n/a
23	TCF12	chr2:10857532-10858370	SK-N-SH	brain:	n/a	n/a
24	FOSL2	chr2:10857716-10858217	SK-N-SH	brain:	n/a	n/a
25	TEAD4	chr2:10857635-10858270	SK-N-SH	brain:	n/a	n/a
26	MYC	chr2:10857559-10858517	MCF10A-Er-Src	breast:	n/a	chr2:10857713-10857724
27	GTF2F1	chr2:10857686-10857948	Hela-S3	cervix:	n/a	n/a
28	RCOR1	chr2:10857748-10858148	Hela-S3	cervix:	n/a	n/a
29	STAT3	chr2:10857625-10858182	MCF10A-Er-Src	breast:	n/a	n/a
30	MAX	chr2:10857714-10858032	Hela-S3	cervix:	n/a	n/a
31	USF2	chr2:10857680-10858063	Hela-S3	cervix:	n/a	n/a
32	FOS	chr2:10857657-10858179	MCF10A-Er-Src	breast:	n/a	n/a
33	SMC3	chr2:10857746-10858017	Hela-S3	cervix:	n/a	n/a
34	CEBPB	chr2:10857696-10858140	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr2:10857707-10858103	HUVEC	blood vessel:	n/a	n/a
36	TCF12	chr2:10857640-10858101	ECC-1	luminal epithelium:	n/a	n/a
37	TCF12	chr2:10857504-10858369	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:10857464..10859699-chr2:10860592..10863283,2	MCF-7	breast:

Variant related genes	Relation type
ATP6V1C2	TF binding region
ENSG00000236162	TF binding region
ENSG00000143882	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1012580	0.87[MEX][hapmap]
rs12993133	0.81[MEX][hapmap]
rs13010024	0.84[EUR][1000 genomes]
rs2287059	0.81[MEX][hapmap]
rs55961697	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56070026	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728944	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73915099	0.81[AMR][1000 genomes]
rs73917905	0.85[AMR][1000 genomes]
rs7578338	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1000953	chr2:10717304-10921805	Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv535584	chr2:10717304-10921805	Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv833381	chr2:10723465-10911284	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1000731	chr2:10758657-10943882	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6736664	C2orf50	cis	cerebellum	SCAN
rs6736664	CYS1	cis	cerebellum	SCAN
rs6736664	PQLC3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10855000-10858600	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr2:10856800-10858200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:10856800-10858400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:10856800-10858600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:10857000-10858600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:10857200-10857800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:10857200-10858600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:10857200-10858600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr2:10857200-10858600	Enhancers	HSMMtube	muscle
10	chr2:10857200-10859200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr2:10857400-10857800	Enhancers	NH-A	brain
12	chr2:10857400-10858400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:10857400-10858400	Enhancers	HSMM	muscle
14	chr2:10857400-10858400	Enhancers	NHDF-Ad	bronchial
15	chr2:10857400-10858600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:10857400-10858600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:10857600-10857800	Bivalent Enhancer	Fetal Muscle Leg	muscle
18	chr2:10857600-10857800	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr2:10857600-10858000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:10857600-10858000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:10857600-10858000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:10857600-10858000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:10857600-10858000	Enhancers	Aorta	Aorta
24	chr2:10857600-10858000	Enhancers	Colon Smooth Muscle	Colon
25	chr2:10857600-10858000	Enhancers	Placenta	Placenta
26	chr2:10857600-10858000	Flanking Active TSS	Hela-S3	cervix
27	chr2:10857600-10858000	Flanking Active TSS	HMEC	breast
28	chr2:10857600-10858000	Flanking Active TSS	NHEK	skin
29	chr2:10857600-10858000	Flanking Active TSS	Osteobl	bone
30	chr2:10857600-10858200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:10857600-10858200	Enhancers	A549	lung
32	chr2:10857600-10858400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr2:10857600-10858400	Flanking Active TSS	HUVEC	blood vessel
34	chr2:10857600-10858400	Enhancers	NHLF	lung

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