Variant report

Variant	rs35020344
Chromosome Location	chr14:64855425-64855426
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	POLR2A	chr14:64853831-64856170	SK-N-MC	brain:	n/a	n/a
2	MAX	chr14:64853990-64855903	Hela-S3	cervix:	n/a	chr14:64855054-64855064 chr14:64855052-64855062 chr14:64855052-64855067 chr14:64854209-64854216 chr14:64855050-64855065 chr14:64855055-64855062 chr14:64855053-64855064 chr14:64854327-64854336 chr14:64855054-64855063 chr14:64854250-64854259
3	TBP	chr14:64853996-64855855	K562	blood:	n/a	n/a
4	POLR2A	chr14:64853709-64855679	GM12878	blood:	n/a	n/a
5	MAFK	chr14:64854540-64855568	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr14:64853980-64855501	GM18526	blood:	n/a	n/a
7	MXI1	chr14:64853786-64856237	SK-N-SH	brain:	n/a	chr14:64855055-64855064
8	POLR2A	chr14:64853659-64856145	GM12892	blood:	n/a	n/a
9	POLR2A	chr14:64853777-64855811	GM12891	blood:	n/a	n/a
10	FOXM1	chr14:64854014-64855439	GM12878	blood:	n/a	n/a
11	STAT5A	chr14:64854813-64855976	GM12878	blood:	n/a	n/a
12	TAF1	chr14:64853844-64855860	H1-hESC	embryonic stem cell:	n/a	n/a
13	E2F4	chr14:64854439-64855471	K562	blood:	n/a	chr14:64854852-64854861 chr14:64854748-64854757 chr14:64854822-64854829 chr14:64854530-64854540 chr14:64854687-64854695 chr14:64854524-64854538 chr14:64854805-64854816 chr14:64854687-64854695 chr14:64854807-64854814 chr14:64854974-64854983 chr14:64854807-64854814 chr14:64855016-64855025 chr14:64854806-64854815 chr14:64854807-64854814
14	POLR2A	chr14:64853846-64855463	K562	blood:	n/a	n/a
15	NFE2	chr14:64855350-64855487	GM12878	blood:	n/a	chr14:64855384-64855394
16	SIN3AK20	chr14:64854896-64855755	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr14:64853961-64855749	HepG2	liver:	n/a	n/a
18	POLR2A	chr14:64853955-64855499	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr14:64853976-64855469	A549	lung:	n/a	n/a
20	MAX	chr14:64853929-64855636	SK-N-SH	brain:	n/a	chr14:64855054-64855064 chr14:64855052-64855062 chr14:64855052-64855067 chr14:64854209-64854216 chr14:64855050-64855065 chr14:64855055-64855062 chr14:64855053-64855064 chr14:64854327-64854336 chr14:64855054-64855063 chr14:64854250-64854259
21	GABPA	chr14:64854342-64855712	MCF-7	breast:	n/a	chr14:64855006-64855015 chr14:64854970-64854984 chr14:64855015-64855026 chr14:64854973-64854982 chr14:64854975-64854984 chr14:64854973-64854984 chr14:64855015-64855029
22	MYC	chr14:64854345-64855569	K562	blood:	n/a	chr14:64855054-64855064 chr14:64855052-64855062 chr14:64855052-64855067 chr14:64855050-64855065 chr14:64855055-64855062 chr14:64855053-64855064 chr14:64855054-64855063
23	BHLHE40	chr14:64854403-64855459	K562	blood:	n/a	n/a
24	POLR2A	chr14:64853889-64855527	GM12878	blood:	n/a	n/a
25	POLR2A	chr14:64854285-64855446	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr14:64853904-64855504	GM19193	blood:	n/a	n/a
27	TBL1XR1	chr14:64854629-64855573	K562	blood:	n/a	n/a
28	MAX	chr14:64853976-64855598	K562	blood:	n/a	chr14:64855054-64855064 chr14:64855052-64855062 chr14:64855052-64855067 chr14:64854209-64854216 chr14:64855050-64855065 chr14:64855055-64855062 chr14:64855053-64855064 chr14:64854327-64854336 chr14:64855054-64855063 chr14:64854250-64854259
29	NFATC1	chr14:64853859-64855449	GM12878	blood:	n/a	n/a
30	MAX	chr14:64853892-64855599	HepG2	liver:	n/a	chr14:64855054-64855064 chr14:64855052-64855062 chr14:64855052-64855067 chr14:64854209-64854216 chr14:64855050-64855065 chr14:64855055-64855062 chr14:64855053-64855064 chr14:64854327-64854336 chr14:64855054-64855063 chr14:64854250-64854259
31	RUNX3	chr14:64854088-64855669	GM12878	blood:	n/a	n/a
32	HEY1	chr14:64853964-64855564	HepG2	liver:	n/a	n/a
33	ELF1	chr14:64854002-64855535	GM12878	blood:	n/a	n/a
34	POLR2A	chr14:64853995-64855940	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr14:64853901-64855563	Raji	blood:	n/a	n/a
36	E2F6	chr14:64853957-64855569	A549	lung:	n/a	chr14:64854852-64854861 chr14:64854748-64854757 chr14:64854822-64854829 chr14:64854530-64854540 chr14:64854687-64854695 chr14:64854524-64854538 chr14:64854687-64854695 chr14:64854807-64854814 chr14:64854974-64854983 chr14:64854807-64854814 chr14:64855016-64855025 chr14:64854806-64854815 chr14:64854807-64854814
37	RELA	chr14:64854024-64855809	GM19099	blood:	n/a	n/a
38	CHD2	chr14:64854086-64855725	Hela-S3	cervix:	n/a	chr14:64854822-64854829
39	POLR2A	chr14:64853710-64856189	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr14:64854917-64855535	GM12891	blood:	n/a	n/a
41	POLR2A	chr14:64853897-64855480	MCF-7	breast:	n/a	n/a
42	YY1	chr14:64854274-64855478	GM12878	blood:	n/a	n/a
43	POLR2A	chr14:64854877-64855478	U87	brain:	n/a	n/a
44	YY1	chr14:64854976-64855542	GM12878	blood:	n/a	n/a
45	FOXM1	chr14:64854351-64855535	GM12878	blood:	n/a	n/a
46	TCF7L2	chr14:64854609-64855501	Hela-S3	cervix:	n/a	n/a
47	MAX	chr14:64853967-64856049	ECC-1	luminal epithelium:	n/a	chr14:64855054-64855064 chr14:64855052-64855062 chr14:64855052-64855067 chr14:64854209-64854216 chr14:64855050-64855065 chr14:64855055-64855062 chr14:64855053-64855064 chr14:64854327-64854336 chr14:64855054-64855063 chr14:64854250-64854259
48	CTCF	chr14:64855320-64855470	HEEpiC	esophagus:	n/a	n/a
49	POLR2A	chr14:64853838-64855898	GM18505	blood:	n/a	n/a
50	BCL3	chr14:64854854-64855458	A549	lung:	n/a	chr14:64855378-64855391

No.	Distal block	Cell Line	Cell type
1	chr14:64853586..64859592-chr14:64968792..64973445,7	MCF-7	breast:
2	chr14:64853592..64856673-chr14:64970174..64974352,5	K562	blood:
3	chr14:64853142..64856847-chr14:64968558..64973163,8	K562	blood:
4	chr14:64853920..64855626-chr14:65380962..65383011,2	MCF-7	breast:
5	chr14:64853800..64856722-chr14:64883915..64886482,2	MCF-7	breast:
6	chr14:64853000..64857077-chr14:64970157..64972159,5	MCF-7	breast:
7	chr14:64805277..64807089-chr14:64853827..64855475,2	MCF-7	breast:
8	chr14:64803480..64807605-chr14:64853546..64855883,4	K562	blood:
9	chr14:64853961..64855505-chr14:64914376..64916038,2	K562	blood:
10	chr14:64854828..64855596-chr3:56716887..56717549,2	HCT-116	colon:
11	chr14:64804489..64807619-chr14:64853862..64856673,3	MCF-7	breast:

Variant related genes	Relation type
MTHFD1	TF binding region
ENSG00000140009	Chromatin interaction
ENSG00000100714	Chromatin interaction
ENSG00000258824	Chromatin interaction
ENSG00000214770	Chromatin interaction
ENSG00000089775	Chromatin interaction
ENSG00000163946	Chromatin interaction
ENSG00000125954	Chromatin interaction
ENSG00000126804	Chromatin interaction
ENSG00000258289	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1076991	0.82[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs11158538	0.82[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs12434608	0.96[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1256093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1256095	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1256097	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1256099	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1256100	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1256101	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1256102	0.89[EUR][1000 genomes]
rs1256107	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1256108	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1256109	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1256110	0.87[CEU][hapmap]
rs1256111	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1256112	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1256113	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1262246	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1270057	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12886138	0.95[ASN][1000 genomes]
rs12889097	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12894546	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2983733	0.87[TSI][hapmap]
rs2983736	0.84[MEX][hapmap];0.87[TSI][hapmap]
rs2983741	0.82[EUR][1000 genomes]
rs2983742	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2987969	0.85[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap]
rs2987979	0.87[TSI][hapmap]
rs3020436	0.83[MEX][hapmap];0.87[TSI][hapmap]
rs3020445	0.90[JPT][hapmap]
rs36016358	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4243628	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57087457	0.82[EUR][1000 genomes]
rs7151163	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8010584	0.81[EUR][1000 genomes]
rs8011386	1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs35020344	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs35020344	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL
rs35020344	MTHFD1	cis	cerebellum	SCAN
rs35020344	MTHFD1	cis	Skin Sun Exposed Lower leg	GTEx
rs35020344	MTHFD1	cis	Thyroid	GTEx
rs35020344	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs35020344	MTHFD1	cis	parietal	SCAN
rs35020344	KCNH5	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64852600-64857000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr14:64852800-64856800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr14:64853000-64857000	Active TSS	K562	blood
4	chr14:64853200-64856600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr14:64853200-64856600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr14:64853200-64856800	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr14:64853400-64856600	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr14:64853400-64857000	Active TSS	H1 Cell Line	embryonic stem cell
9	chr14:64853800-64855600	Active TSS	Brain Germinal Matrix	brain
10	chr14:64853800-64855600	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr14:64853800-64855800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr14:64853800-64855800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr14:64853800-64855800	Active TSS	Colon Smooth Muscle	Colon
14	chr14:64853800-64855800	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr14:64853800-64855800	Active TSS	Fetal Kidney	kidney
16	chr14:64853800-64855800	Active TSS	Fetal Stomach	stomach
17	chr14:64853800-64856200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr14:64853800-64856200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr14:64853800-64856200	Active TSS	Esophagus	oesophagus
20	chr14:64853800-64856200	Active TSS	Fetal Intestine Large	intestine
21	chr14:64853800-64856200	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr14:64853800-64856400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr14:64853800-64856400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr14:64853800-64856400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr14:64853800-64856400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr14:64853800-64856400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr14:64853800-64856400	Active TSS	Thymus	Thymus
28	chr14:64853800-64856600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr14:64853800-64856600	Active TSS	H9 Cell Line	embryonic stem cell
30	chr14:64853800-64856600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr14:64853800-64856600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr14:64853800-64856600	Active TSS	A549	lung
33	chr14:64853800-64856600	Active TSS	HSMM	muscle
34	chr14:64853800-64856600	Active TSS	NHDF-Ad	bronchial
35	chr14:64854000-64855600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr14:64854000-64855600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr14:64854000-64855600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr14:64854000-64855600	Active TSS	Brain Substantia Nigra	brain
39	chr14:64854000-64855600	Active TSS	Lung	lung
40	chr14:64854000-64855800	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr14:64854000-64855800	Active TSS	Gastric	stomach
42	chr14:64854000-64856000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr14:64854000-64856000	Active TSS	Pancreas	Pancrea
44	chr14:64854000-64856200	Active TSS	Aorta	Aorta
45	chr14:64854000-64856200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr14:64854000-64856200	Active TSS	Ovary	ovary
47	chr14:64854000-64856200	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr14:64854000-64856200	Active TSS	HSMMtube	muscle
49	chr14:64854000-64856400	Active TSS	Right Atrium	heart
50	chr14:64854000-64857000	Active TSS	iPS-20b Cell Line	embryonic stem cell

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