Variant report

Variant	rs661755
Chromosome Location	chr1:210001173-210001174
allele	C/T
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	chr1:210000884-210001681	A549	lung:	n/a	n/a
2	ELF1	chr1:210001015-210001871	GM12878	blood:	n/a	n/a
3	CTCF	chr1:210001093-210001406	HepG2	liver:	n/a	n/a
4	CEBPB	chr1:210001010-210001822	Hela-S3	cervix:	n/a	n/a
5	TAF1	chr1:210001126-210001460	GM12891	blood:	n/a	n/a
6	MXI1	chr1:210000798-210001833	IMR90	lung:	n/a	n/a
7	CTCF	chr1:210001160-210001310	HUVEC	blood vessel:	n/a	n/a
8	STAT3	chr1:210001117-210001412	MCF10A-Er-Src	breast:	n/a	n/a
9	GABPA	chr1:210001066-210001439	GM12878	blood:	n/a	n/a
10	SIX5	chr1:210001098-210001441	GM12878	blood:	n/a	n/a
11	FOSL2	chr1:210000918-210001715	A549	lung:	n/a	chr1:210001593-210001607
12	TAF1	chr1:210001051-210001545	H1-neurons	neurons:	n/a	n/a
13	CHD2	chr1:210000922-210001792	GM12878	blood:	n/a	n/a
14	ATF1	chr1:210000805-210001500	K562	blood:	n/a	n/a
15	CTCF	chr1:210001160-210001310	AG04449	skin:	n/a	n/a
16	CTCF	chr1:210001160-210001310	HCPEpiC	choroid plexus:	n/a	n/a
17	GATA1	chr1:209999983-210001849	K562	blood:	n/a	chr1:210001706-210001716
18	TEAD4	chr1:210000754-210001649	K562	blood:	n/a	n/a
19	USF1	chr1:210001127-210001503	SK-N-SH_RA	brain:	n/a	n/a
20	GABPA	chr1:210000922-210001639	MCF-7	breast:	n/a	n/a
21	POLR2A	chr1:210000892-210001563	HepG2	liver:	n/a	n/a
22	MAX	chr1:210001041-210001683	GM12878	blood:	n/a	chr1:210001329-210001338 chr1:210001329-210001339 chr1:210001327-210001342 chr1:210001330-210001337 chr1:210001328-210001339 chr1:210001328-210001338
23	GTF3C2	chr1:210000384-210001847	K562	blood:	n/a	n/a
24	CEBPD	chr1:210001044-210001381	HepG2	liver:	n/a	n/a
25	MYC	chr1:210001053-210001587	HepG2	liver:	n/a	chr1:210001329-210001338 chr1:210001329-210001339 chr1:210001327-210001342 chr1:210001330-210001337 chr1:210001328-210001339 chr1:210001328-210001338
26	SPI1	chr1:210001105-210001429	HL-60	blood:	n/a	n/a
27	E2F6	chr1:210000956-210001712	K562	blood:	n/a	n/a
28	EP300	chr1:210000720-210001704	K562	blood:	n/a	n/a
29	PML	chr1:210000804-210001618	K562	blood:	n/a	n/a
30	POLR2A	chr1:210000959-210001609	H1-neurons	neurons:	n/a	n/a
31	POLR2A	chr1:210000963-210001551	GM12891	blood:	n/a	n/a
32	CTCF	chr1:210001080-210001344	SK-N-SH_RA	brain:	n/a	n/a
33	CTCF	chr1:210001140-210001290	GM12875	blood:	n/a	n/a
34	HCFC1	chr1:210000804-210001945	Hela-S3	cervix:	n/a	n/a
35	GTF2F1	chr1:210000897-210001522	K562	blood:	n/a	n/a
36	E2F6	chr1:210000925-210001792	H1-hESC	embryonic stem cell:	n/a	n/a
37	MBD4	chr1:210000975-210001580	HepG2	liver:	n/a	n/a
38	TAF1	chr1:210001061-210001250	GM12878	blood:	n/a	n/a
39	TAF1	chr1:210001088-210001388	PFSK-1	brain:	n/a	n/a
40	ZNF384	chr1:210001100-210001911	GM12878	blood:	n/a	n/a
41	RELA	chr1:210000978-210001661	GM18951	blood:	n/a	n/a
42	CEBPB	chr1:210000770-210001554	K562	blood:	n/a	n/a
43	RCOR1	chr1:210000243-210001790	K562	blood:	n/a	n/a
44	EGR1	chr1:210000941-210001432	K562	blood:	n/a	n/a
45	ATF3	chr1:210001076-210001441	GM12878	blood:	n/a	n/a
46	POLR2A	chr1:210000859-210001710	PANC-1	pancreas:	n/a	n/a
47	PML	chr1:210001065-210001481	GM12878	blood:	n/a	n/a
48	MXI1	chr1:210000887-210001789	K562	blood:	n/a	n/a
49	REST	chr1:210001139-210001441	Hela-S3	cervix:	n/a	n/a
50	CTCF	chr1:210001068-210001404	GM19238	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:209999396..210002885-chr1:210546190..210548808,3	K562	blood:
2	chr1:209995353..209998573-chr1:209998823..210001196,6	K562	blood:
3	chr1:209977871..209984485-chr1:209998424..210002427,6	K562	blood:
4	chr1:209956517..209958141-chr1:209999783..210001469,2	MCF-7	breast:
5	chr1:209977871..209981214-chr1:209999703..210002866,6	K562	blood:
6	chr1:209999584..210001298-chr1:210028865..210031163,2	K562	blood:
7	chr1:209991113..209993100-chr1:209999001..210001316,2	K562	blood:
8	chr1:209839849..209842808-chr1:209998305..210001255,2	K562	blood:
9	chr1:210000759..210001556-chr13:31039833..31040722,2	NB4	blood:

Variant related genes	Relation type
DIEXF	TF binding region
ENSG00000189403	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000117595	Chromatin interaction
ENSG00000162757	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11579771	1.00[CEU][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2049997	0.83[AMR][1000 genomes]
rs2236906	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2357231	0.96[YRI][hapmap]
rs3753516	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4844497	0.83[AMR][1000 genomes]
rs583814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs585191	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs593543	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs596731	0.81[EUR][1000 genomes]
rs597673	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs599021	0.94[ASN][1000 genomes]
rs599663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs615276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623360	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs632305	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648349	0.92[ASN][1000 genomes]
rs651141	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs684083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs846808	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs861019	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs661755	SYT14	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210000400-210002400	Active TSS	A549	lung
2	chr1:210000600-210002000	Active TSS	Colonic Mucosa	Colon
3	chr1:210000600-210002200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:210000600-210002400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:210000600-210002400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:210000600-210002400	Active TSS	Right Atrium	heart
7	chr1:210000600-210002600	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr1:210000600-210002600	Active TSS	K562	blood
9	chr1:210000800-210001200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:210000800-210001200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:210000800-210001200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr1:210000800-210001200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
13	chr1:210000800-210001200	Flanking Active TSS	Primary B cells from peripheral blood	blood
14	chr1:210000800-210001200	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr1:210000800-210001200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr1:210000800-210001200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr1:210000800-210001200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr1:210000800-210001200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:210000800-210001200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr1:210000800-210001200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:210000800-210001200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr1:210000800-210001200	Flanking Active TSS	HMEC	breast
23	chr1:210000800-210001200	Flanking Active TSS	HUVEC	blood vessel
24	chr1:210000800-210001200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr1:210000800-210001200	Flanking Active TSS	NH-A	brain
26	chr1:210000800-210001200	Flanking Active TSS	NHEK	skin
27	chr1:210000800-210001600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:210000800-210001600	Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr1:210000800-210001800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr1:210000800-210002000	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr1:210000800-210002000	Active TSS	H1 Cell Line	embryonic stem cell
32	chr1:210000800-210002000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:210000800-210002000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:210000800-210002000	Active TSS	H9 Cell Line	embryonic stem cell
35	chr1:210000800-210002000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:210000800-210002000	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr1:210000800-210002000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:210000800-210002000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr1:210000800-210002000	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr1:210000800-210002000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:210000800-210002000	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr1:210000800-210002000	Active TSS	Aorta	Aorta
43	chr1:210000800-210002000	Active TSS	Brain Angular Gyrus	brain
44	chr1:210000800-210002000	Active TSS	Brain Anterior Caudate	brain
45	chr1:210000800-210002000	Active TSS	Brain Cingulate Gyrus	brain
46	chr1:210000800-210002000	Active TSS	Brain Hippocampus Middle	brain
47	chr1:210000800-210002000	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr1:210000800-210002000	Active TSS	Brain Substantia Nigra	brain
49	chr1:210000800-210002000	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr1:210000800-210002000	Active TSS	Esophagus	oesophagus

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