Variant report

Variant	rs2276856
Chromosome Location	chr3:46037405-46037406
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	chr3:46036964-46037503	Hela-S3	cervix:	n/a	n/a
2	MYC	chr3:46037183-46037502	MCF-7	breast:	n/a	n/a
3	CEBPB	chr3:46037156-46037481	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:46036930-46037574	HUVEC	blood vessel:	n/a	n/a
5	MAZ	chr3:46036305-46037637	Hela-S3	cervix:	n/a	chr3:46036468-46036478 chr3:46036480-46036496 chr3:46036471-46036478 chr3:46036529-46036539 chr3:46036469-46036478
6	NFIC	chr3:46037004-46037684	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:46036358-46037508	K562	blood:	n/a	n/a
8	ZNF263	chr3:46036724-46037960	HEK293-T-REx	kidney:	n/a	n/a
9	EGR1	chr3:46037075-46037600	ECC-1	luminal epithelium:	n/a	chr3:46037318-46037328 chr3:46037393-46037417 chr3:46037361-46037385 chr3:46037439-46037446 chr3:46037327-46037351 chr3:46037318-46037327 chr3:46037415-46037425 chr3:46037316-46037330
10	CREB1	chr3:46036849-46037745	K562	blood:	n/a	n/a
11	CTCFL	chr3:46037240-46037481	K562	blood:	n/a	n/a
12	POLR2A	chr3:46036853-46037581	MCF-7	breast:	n/a	n/a
13	POLR2A	chr3:46036197-46037631	GM19193	blood:	n/a	n/a
14	POLR2A	chr3:46036532-46037523	GM12878	blood:	n/a	n/a
15	ZBTB7A	chr3:46036668-46037688	ECC-1	luminal epithelium:	n/a	n/a
16	TAF1	chr3:46037079-46037423	GM12878	blood:	n/a	n/a
17	ELF1	chr3:46036524-46037601	GM12878	blood:	n/a	chr3:46036933-46036945
18	TAF1	chr3:46037025-46037444	Hela-S3	cervix:	n/a	n/a
19	EBF1	chr3:46037118-46037539	GM12878	blood:	n/a	n/a
20	ELK1	chr3:46037172-46037714	Hela-S3	cervix:	n/a	n/a
21	CHD2	chr3:46037094-46037570	K562	blood:	n/a	n/a
22	MAFK	chr3:46037160-46037644	K562	blood:	n/a	n/a
23	MYC	chr3:46037391-46037422	MCF-7	breast:	n/a	n/a
24	TCF12	chr3:46037028-46037553	ECC-1	luminal epithelium:	n/a	chr3:46037172-46037182
25	MAX	chr3:46036754-46037844	HepG2	liver:	n/a	n/a
26	RAD21	chr3:46036619-46037481	IMR90	lung:	n/a	chr3:46036933-46036945 chr3:46036740-46036752
27	YY1	chr3:46036712-46037585	GM12892	blood:	n/a	chr3:46037317-46037326
28	BRCA1	chr3:46037308-46037484	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAZ	chr3:46037197-46037598	HepG2	liver:	n/a	n/a
30	MYC	chr3:46037188-46037444	K562	blood:	n/a	n/a
31	CUX1	chr3:46037087-46037655	K562	blood:	n/a	n/a
32	STAT3	chr3:46037393-46037426	MCF10A-Er-Src	breast:	n/a	n/a
33	EGR1	chr3:46036870-46037457	K562	blood:	n/a	chr3:46037318-46037328 chr3:46037393-46037417 chr3:46037361-46037385 chr3:46037439-46037446 chr3:46037327-46037351 chr3:46037318-46037327 chr3:46037415-46037425 chr3:46037316-46037330
34	POLR2A	chr3:46037063-46037555	HUVEC	blood vessel:	n/a	n/a
35	POU2F2	chr3:46037000-46037485	GM12878	blood:	n/a	n/a
36	SIX5	chr3:46037082-46037576	A549	lung:	n/a	chr3:46037328-46037337 chr3:46037330-46037339 chr3:46037396-46037405 chr3:46037394-46037403
37	EBF1	chr3:46036898-46037412	GM12878	blood:	n/a	n/a
38	FOXP2	chr3:46036985-46037545	PFSK-1	brain:	n/a	n/a
39	POLR2A	chr3:46036592-46037621	K562	blood:	n/a	n/a
40	POLR2A	chr3:46036768-46037678	HCT-116	colon:	n/a	n/a
41	YY1	chr3:46036948-46037601	SK-N-SH	brain:	n/a	chr3:46037317-46037326
42	POLR2A	chr3:46036142-46037405	GM12878	blood:	n/a	n/a
43	SP1	chr3:46036994-46037599	GM12878	blood:	n/a	chr3:46037094-46037106 chr3:46037095-46037104 chr3:46037417-46037426 chr3:46037319-46037330
44	USF2	chr3:46037095-46037547	GM12878	blood:	n/a	n/a
45	RCOR1	chr3:46036900-46037593	K562	blood:	n/a	n/a
46	SMARCC2	chr3:46036697-46037509	Hela-S3	cervix:	n/a	chr3:46037394-46037403 chr3:46037328-46037337
47	HCFC1	chr3:46036468-46038390	Hela-S3	cervix:	n/a	n/a
48	ELK1	chr3:46036979-46037454	K562	blood:	n/a	n/a
49	NFIC	chr3:46037099-46037635	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr3:46036558-46037433	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:5389674..5390238-chr3:46037073..46037659,2	Hela-S3	cervix:
2	chr3:45979978..45982491-chr3:46035904..46038054,2	MCF-7	breast:
3	chr3:46036059..46037983-chr3:46447594..46449867,2	K562	blood:

Variant related genes	Relation type
FYCO1	TF binding region
ENSG00000121797	Chromatin interaction
ENSG00000167842	Chromatin interaction
ENSG00000072849	Chromatin interaction
ENSG00000223552	Chromatin interaction
ENSG00000172215	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs13064616	0.82[ASN][1000 genomes]
rs13074382	0.90[YRI][hapmap]
rs13081213	0.90[YRI][hapmap]
rs13090194	0.90[YRI][hapmap]
rs1392288	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1463680	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1500003	0.82[ASN][1000 genomes]
rs1846615	0.82[ASN][1000 genomes]
rs1873001	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2102055	0.90[YRI][hapmap]
rs2129879	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2129881	0.82[ASN][1000 genomes]
rs2133660	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2171528	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2171529	0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2230322	0.90[YRI][hapmap]
rs2276855	0.86[ASN][1000 genomes]
rs35669129	0.90[YRI][hapmap]
rs3796374	0.82[ASN][1000 genomes]
rs3947589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4683165	0.82[ASN][1000 genomes]
rs55844314	0.82[ASN][1000 genomes]
rs57651127	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57837898	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs751667	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7612402	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9844821	0.82[ASN][1000 genomes]
rs9875616	1.00[CHB][hapmap];1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv1805205	chr3:46032847-46111081	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2276856	FYCO1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46035800-46037600	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr3:46035800-46037800	Active TSS	Right Atrium	heart
3	chr3:46036000-46037600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:46036000-46037600	Active TSS	Aorta	Aorta
5	chr3:46036000-46037600	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr3:46036000-46037600	Active TSS	Ovary	ovary
7	chr3:46036000-46037600	Active TSS	Hela-S3	cervix
8	chr3:46036000-46037800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr3:46036000-46037800	Active TSS	Colonic Mucosa	Colon
10	chr3:46036000-46037800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr3:46036000-46037800	Active TSS	Right Ventricle	heart
12	chr3:46036000-46038000	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr3:46036200-46037600	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr3:46036200-46037600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:46036200-46037600	Active TSS	Fetal Intestine Large	intestine
16	chr3:46036200-46037600	Active TSS	Gastric	stomach
17	chr3:46036200-46037800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:46036200-46037800	Active TSS	H9 Cell Line	embryonic stem cell
19	chr3:46036200-46037800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:46036200-46037800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:46036200-46037800	Active TSS	Psoas Muscle	Psoas
22	chr3:46036200-46038000	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr3:46036200-46038000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:46036200-46038000	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr3:46036200-46038000	Active TSS	Fetal Kidney	kidney
26	chr3:46036200-46038000	Active TSS	A549	lung
27	chr3:46036400-46037600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:46036400-46037600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:46036400-46037600	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr3:46036400-46037600	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr3:46036400-46037600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:46036400-46037600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:46036400-46037600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:46036400-46037600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:46036400-46037600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:46036400-46037600	Active TSS	Brain Angular Gyrus	brain
37	chr3:46036400-46037600	Active TSS	Brain Anterior Caudate	brain
38	chr3:46036400-46037600	Active TSS	Brain Cingulate Gyrus	brain
39	chr3:46036400-46037600	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr3:46036400-46037600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:46036400-46037600	Active TSS	Brain Substantia Nigra	brain
42	chr3:46036400-46037600	Active TSS	Colon Smooth Muscle	Colon
43	chr3:46036400-46037600	Active TSS	Duodenum Mucosa	Duodenum
44	chr3:46036400-46037600	Active TSS	Fetal Heart	heart
45	chr3:46036400-46037600	Active TSS	Fetal Stomach	stomach
46	chr3:46036400-46037600	Active TSS	Lung	lung
47	chr3:46036400-46037600	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr3:46036400-46037600	Active TSS	NHLF	lung
49	chr3:46036400-46037800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:46036400-46037800	Active TSS	iPS-15b Cell Line	embryonic stem cell

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