Variant report

Variant	rs518793
Chromosome Location	chr1:212588206-212588207
allele	C/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	NRF1	chr1:212588062-212588462	H1-hESC	embryonic stem cell:	n/a	chr1:212588245-212588259 chr1:212588250-212588259 chr1:212588247-212588258 chr1:212588248-212588257 chr1:212588248-212588259
2	MYC	chr1:212587629-212589222	NB4	blood:	n/a	chr1:212588309-212588319 chr1:212587669-212587679
3	MXI1	chr1:212588067-212588551	K562	blood:	n/a	n/a
4	TCF12	chr1:212587626-212588635	ECC-1	luminal epithelium:	n/a	n/a
5	ETS1	chr1:212587912-212588599	K562	blood:	n/a	chr1:212588295-212588308 chr1:212588411-212588424 chr1:212588415-212588422 chr1:212588411-212588422 chr1:212588296-212588309 chr1:212588409-212588423 chr1:212588411-212588426
6	BCLAF1	chr1:212587946-212588696	GM12878	blood:	n/a	chr1:212588411-212588420 chr1:212587983-212587992 chr1:212588261-212588274
7	CTCF	chr1:212588140-212588290	GM12871	blood:	n/a	n/a
8	BRCA1	chr1:212588145-212588322	HepG2	liver:	n/a	n/a
9	MAX	chr1:212587408-212588556	ECC-1	luminal epithelium:	n/a	chr1:212588309-212588319 chr1:212587669-212587679
10	ZC3H11A	chr1:212588118-212588598	K562	blood:	n/a	n/a
11	TEAD4	chr1:212588004-212589288	K562	blood:	n/a	n/a
12	EP300	chr1:212588106-212588711	GM12878	blood:	n/a	chr1:212588411-212588425
13	TAF7	chr1:212587860-212588535	H1-hESC	embryonic stem cell:	n/a	n/a
14	IRF4	chr1:212588112-212588620	GM12878	blood:	n/a	n/a
15	NANOG	chr1:212588020-212588459	H1-hESC	embryonic stem cell:	n/a	n/a
16	SIN3AK20	chr1:212588018-212588557	H1-hESC	embryonic stem cell:	n/a	n/a
17	CHD2	chr1:212588043-212589141	GM12878	blood:	n/a	n/a
18	TAF1	chr1:212588022-212588584	K562	blood:	n/a	n/a
19	CCNT2	chr1:212587629-212588458	K562	blood:	n/a	n/a
20	MAX	chr1:212587315-212589069	GM12878	blood:	n/a	chr1:212588309-212588319 chr1:212587669-212587679
21	NFIC	chr1:212588085-212589257	GM12878	blood:	n/a	n/a
22	SP1	chr1:212587960-212588593	H1-hESC	embryonic stem cell:	n/a	chr1:212587982-212587994 chr1:212588433-212588445 chr1:212588309-212588318 chr1:212588433-212588445 chr1:212587984-212587993 chr1:212587982-212587994 chr1:212587983-212587992 chr1:212588430-212588444 chr1:212588310-212588319
23	BCLAF1	chr1:212587937-212588751	GM12878	blood:	n/a	chr1:212588411-212588420 chr1:212587983-212587992 chr1:212588261-212588274
24	ETS1	chr1:212588069-212588456	A549	lung:	n/a	chr1:212588295-212588308 chr1:212588411-212588424 chr1:212588415-212588422 chr1:212588411-212588422 chr1:212588296-212588309 chr1:212588409-212588423 chr1:212588411-212588426
25	TBP	chr1:212588137-212588546	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr1:212587894-212588524	HUVEC	blood vessel:	n/a	n/a
27	ETS1	chr1:212587829-212588529	K562	blood:	n/a	chr1:212588295-212588308 chr1:212588411-212588424 chr1:212588415-212588422 chr1:212588411-212588422 chr1:212588296-212588309 chr1:212588409-212588423 chr1:212588411-212588426
28	POLR2A	chr1:212588078-212588230	IMR90	lung:	n/a	n/a
29	POLR2A	chr1:212587902-212588676	GM12891	blood:	n/a	n/a
30	YY1	chr1:212588043-212588445	SK-N-SH_RA	brain:	n/a	chr1:212588261-212588272 chr1:212588312-212588321
31	TAF1	chr1:212587956-212588586	GM12878	blood:	n/a	n/a
32	HMGN3	chr1:212587519-212588498	K562	blood:	n/a	n/a
33	IRF1	chr1:212588108-212588641	K562	blood:	n/a	chr1:212588412-212588421 chr1:212588455-212588469
34	POLR2A	chr1:212587987-212588470	A549	lung:	n/a	n/a
35	SIX5	chr1:212587987-212588539	A549	lung:	n/a	chr1:212588296-212588305 chr1:212588295-212588309 chr1:212588298-212588307
36	FOXM1	chr1:212588165-212588626	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:212587999-212588638	K562	blood:	n/a	n/a
38	POLR2A	chr1:212587991-212588642	K562	blood:	n/a	n/a
39	SPI1	chr1:212588157-212588673	GM12878	blood:	n/a	chr1:212588413-212588426 chr1:212588507-212588516 chr1:212588508-212588515 chr1:212588414-212588427 chr1:212588416-212588423 chr1:212588411-212588420
40	POLR2A	chr1:212587788-212588758	K562	blood:	n/a	n/a
41	HCFC1	chr1:212587426-212589189	K562	blood:	n/a	n/a
42	POLR2A	chr1:212587484-212589250	GM12878	blood:	n/a	n/a
43	BHLHE40	chr1:212588084-212588543	HepG2	liver:	n/a	chr1:212588255-212588271
44	SP1	chr1:212587998-212588495	A549	lung:	n/a	chr1:212588433-212588445 chr1:212588309-212588318 chr1:212588433-212588445 chr1:212588430-212588444 chr1:212588310-212588319
45	POLR2A	chr1:212587924-212588296	U87	brain:	n/a	n/a
46	POLR2A	chr1:212587756-212588609	PFSK-1	brain:	n/a	n/a
47	POLR2A	chr1:212587965-212588610	HepG2	liver:	n/a	n/a
48	YY1	chr1:212588087-212588578	GM12878	blood:	n/a	chr1:212588261-212588272 chr1:212588312-212588321
49	POLR2A	chr1:212587902-212588601	GM10847	blood:	n/a	n/a
50	TCF12	chr1:212587981-212588552	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:212458597..212460542-chr1:212586367..212588357,2	MCF-7	breast:
2	chr1:212587143..212589756-chr1:212965630..212967810,2	K562	blood:
3	chr1:212550848..212553114-chr1:212586010..212588532,2	MCF-7	breast:
4	chr1:212586222..212588940-chr1:212781343..212783037,2	K562	blood:
5	chr1:212586060..212592297-chr1:212603893..212609565,9	MCF-7	breast:
6	chr1:212588056..212590074-chr1:212779163..212783567,3	K562	blood:
7	chr1:212549233..212551182-chr1:212586836..212589324,2	K562	blood:
8	chr1:212587912..212590110-chr1:212604889..212609190,4	K562	blood:
9	chr1:212585974..212594847-chr1:212598812..212609579,19	K562	blood:
10	chr1:212586665..212588349-chr1:212964322..212966191,2	MCF-7	breast:
11	chr1:212581574..212584496-chr1:212586803..212589409,2	MCF-7	breast:

Variant related genes	Relation type
TMEM206	TF binding region
ENSG00000117697	Chromatin interaction
ENSG00000065600	Chromatin interaction
ENSG00000066027	Chromatin interaction
ENSG00000117691	Chromatin interaction
ENSG00000203705	Chromatin interaction
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1086893	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2252044	1.00[YRI][hapmap]
rs3099112	0.92[YRI][hapmap]
rs351393	1.00[YRI][hapmap]
rs3767861	0.84[YRI][hapmap]
rs3767862	0.84[YRI][hapmap]
rs612414	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs701905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7415843	0.92[YRI][hapmap]
rs7519959	0.84[YRI][hapmap]
rs792447	1.00[YRI][hapmap]
rs792448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	esv1828436	chr1:212577765-212591863	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv873156	chr1:212585092-212646225	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs518793	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs518793	NENF	cis	Esophagus Mucosa	GTEx
rs518793	TMEM206	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212587000-212588400	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr1:212587000-212588400	Active TSS	Fetal Kidney	kidney
3	chr1:212587000-212588400	Active TSS	HSMM	muscle
4	chr1:212587000-212588600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr1:212587000-212588800	Enhancers	Fetal Heart	heart
6	chr1:212587000-212589000	Active TSS	Rectal Smooth Muscle	rectum
7	chr1:212587200-212588400	Active TSS	HSMMtube	muscle
8	chr1:212587200-212588600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:212587200-212588600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:212587400-212588400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr1:212587400-212588400	Active TSS	H1 Cell Line	embryonic stem cell
12	chr1:212587400-212588400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:212587400-212588400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:212587400-212588400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:212587400-212588400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:212587400-212588400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:212587400-212588400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:212587400-212588400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:212587400-212588400	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr1:212587400-212588400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:212587400-212588400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:212587400-212588400	Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr1:212587400-212588400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:212587400-212588400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:212587400-212588400	Active TSS	Brain Angular Gyrus	brain
26	chr1:212587400-212588400	Active TSS	Brain Anterior Caudate	brain
27	chr1:212587400-212588400	Active TSS	Brain Hippocampus Middle	brain
28	chr1:212587400-212588400	Active TSS	Colon Smooth Muscle	Colon
29	chr1:212587400-212588400	Active TSS	Esophagus	oesophagus
30	chr1:212587400-212588400	Active TSS	Fetal Intestine Large	intestine
31	chr1:212587400-212588400	Active TSS	Fetal Lung	lung
32	chr1:212587400-212588400	Active TSS	A549	lung
33	chr1:212587400-212588400	Active TSS	NHDF-Ad	bronchial
34	chr1:212587400-212588400	Active TSS	NHLF	lung
35	chr1:212587400-212588400	Active TSS	Osteobl	bone
36	chr1:212587400-212588600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:212587400-212588600	Active TSS	Aorta	Aorta
38	chr1:212587400-212588600	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr1:212587400-212588600	Active TSS	Lung	lung
40	chr1:212587400-212588600	Active TSS	Ovary	ovary
41	chr1:212587400-212588600	Active TSS	Thymus	Thymus
42	chr1:212587400-212588600	Active TSS	GM12878-XiMat	blood
43	chr1:212587400-212589000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:212587600-212588400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:212587600-212588400	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr1:212587600-212588400	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr1:212587600-212588400	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr1:212587600-212588400	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr1:212587600-212588400	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr1:212587600-212588400	Active TSS	Primary hematopoietic stem cells	blood

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