Variant report

Variant	rs6681345
Chromosome Location	chr1:93427347-93427348
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	MAX	chr1:93426829-93427663	SK-N-SH	brain:	n/a	chr1:93427313-93427323
2	RCOR1	chr1:93426780-93427510	K562	blood:	n/a	n/a
3	CTCF	chr1:93427340-93427490	HepG2	liver:	n/a	chr1:93427425-93427438
4	MYC	chr1:93427343-93427493	MCF-7	breast:	n/a	n/a
5	POLR2A	chr1:93427097-93427656	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr1:93427300-93427450	HCPEpiC	choroid plexus:	n/a	chr1:93427425-93427438 chr1:93427316-93427329
7	POLR2A	chr1:93425826-93428558	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:93427066-93427374	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr1:93427040-93427405	K562	blood:	n/a	n/a
10	YY1	chr1:93427075-93427380	SK-N-SH_RA	brain:	n/a	chr1:93427316-93427330 chr1:93427195-93427206 chr1:93427198-93427212 chr1:93427115-93427129 chr1:93427331-93427342 chr1:93427260-93427269
11	MXI1	chr1:93425637-93427664	HepG2	liver:	n/a	n/a
12	POLR2A	chr1:93427090-93427404	HepG2	liver:	n/a	n/a
13	MAX	chr1:93427091-93427551	H1-hESC	embryonic stem cell:	n/a	chr1:93427313-93427323
14	MXI1	chr1:93427195-93427510	H1-hESC	embryonic stem cell:	n/a	n/a
15	E2F6	chr1:93426133-93427751	K562	blood:	n/a	chr1:93426330-93426339 chr1:93426780-93426789 chr1:93427312-93427324
16	POLR2A	chr1:93425974-93428432	GM18526	blood:	n/a	n/a
17	RFX5	chr1:93427144-93427621	Hela-S3	cervix:	n/a	n/a
18	BHLHE40	chr1:93426942-93428033	K562	blood:	n/a	chr1:93427324-93427340 chr1:93427224-93427240 chr1:93427195-93427211 chr1:93427198-93427214
19	POLR2A	chr1:93426497-93427478	HEK293	kidney:	n/a	n/a
20	POLR2A	chr1:93426478-93427604	H1-neurons	neurons:	n/a	n/a
21	ZNF143	chr1:93425894-93427440	GM12878	blood:	n/a	n/a
22	CTCF	chr1:93427266-93427360	GM19238	blood:	n/a	chr1:93427316-93427329
23	ELK1	chr1:93427294-93427798	GM12878	blood:	n/a	n/a
24	RAD21	chr1:93427027-93427381	SK-N-SH_RA	brain:	n/a	n/a
25	PML	chr1:93425555-93428546	GM12878	blood:	n/a	n/a
26	FOXP2	chr1:93426943-93427555	PFSK-1	brain:	n/a	n/a
27	JUND	chr1:93427135-93427719	K562	blood:	n/a	n/a
28	POLR2A	chr1:93426925-93427709	GM12878	blood:	n/a	n/a
29	MAX	chr1:93425813-93427544	HepG2	liver:	n/a	chr1:93427313-93427323
30	CTCF	chr1:93427337-93427392	NHEK	skin:	n/a	n/a
31	SP1	chr1:93427044-93427428	A549	lung:	n/a	chr1:93427173-93427187
32	POLR2A	chr1:93427013-93427488	HUVEC	blood vessel:	n/a	n/a
33	TAF1	chr1:93426562-93427553	HepG2	liver:	n/a	n/a
34	EGR1	chr1:93426914-93427546	K562	blood:	n/a	chr1:93427039-93427049 chr1:93427337-93427346 chr1:93427317-93427330 chr1:93427307-93427320 chr1:93427261-93427275 chr1:93427319-93427329
35	MAZ	chr1:93425647-93428513	IMR90	lung:	n/a	chr1:93427313-93427323 chr1:93428231-93428240
36	MAX	chr1:93425893-93427628	A549	lung:	n/a	chr1:93427313-93427323
37	POLR2A	chr1:93427078-93427365	HCT-116	colon:	n/a	n/a
38	POLR2A	chr1:93427080-93427397	SK-N-SH	brain:	n/a	n/a
39	YY1	chr1:93427016-93427395	SK-N-SH_RA	brain:	n/a	chr1:93427316-93427330 chr1:93427195-93427206 chr1:93427198-93427212 chr1:93427115-93427129 chr1:93427331-93427342 chr1:93427260-93427269
40	POLR2A	chr1:93426663-93427726	MCF-7	breast:	n/a	n/a
41	YY1	chr1:93426851-93428492	GM12878	blood:	n/a	chr1:93427316-93427330 chr1:93427195-93427206 chr1:93427198-93427212 chr1:93426874-93426885 chr1:93427115-93427129 chr1:93427400-93427414 chr1:93427331-93427342 chr1:93427437-93427451 chr1:93427260-93427269
42	MAX	chr1:93425976-93428067	Hela-S3	cervix:	n/a	chr1:93427313-93427323
43	TBL1XR1	chr1:93427266-93427349	K562	blood:	n/a	n/a
44	MAX	chr1:93425879-93428020	A549	lung:	n/a	chr1:93427313-93427323
45	ETS1	chr1:93427127-93427779	GM12878	blood:	n/a	chr1:93427432-93427441
46	POLR2A	chr1:93427068-93427748	GM12878	blood:	n/a	n/a
47	POLR2A	chr1:93426795-93428377	MCF10A-Er-Src	breast:	n/a	n/a
48	CHD2	chr1:93425934-93427636	GM12878	blood:	n/a	n/a
49	YY1	chr1:93427071-93427546	K562	blood:	n/a	chr1:93427316-93427330 chr1:93427195-93427206 chr1:93427198-93427212 chr1:93427115-93427129 chr1:93427400-93427414 chr1:93427331-93427342 chr1:93427437-93427451 chr1:93427260-93427269
50	MAX	chr1:93425890-93427764	ECC-1	luminal epithelium:	n/a	chr1:93427313-93427323

No.	Distal block	Cell Line	Cell type
1	chr1:93425993..93428373-chr1:93433568..93436256,2	MCF-7	breast:
2	chr1:93296297..93299381-chr1:93425183..93428047,4	K562	blood:
3	chr1:93296356..93298770-chr1:93426282..93429088,3	MCF-7	breast:
4	chr1:93323615..93326108-chr1:93427081..93429012,3	K562	blood:
5	chr1:93425058..93429733-chr1:93431759..93435608,8	K562	blood:
6	chr1:93323615..93326108-chr1:93427081..93429012,2	K562	blood:
7	chr1:28831926..28832622-chr1:93426787..93427442,3	Hela-S3	cervix:

Variant related genes	Relation type
FAM69A	TF binding region
ENSG00000242125	Chromatin interaction
ENSG00000122406	Chromatin interaction
ENSG00000180198	Chromatin interaction
ENSG00000252121	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10874752	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11164838	0.83[ASN][1000 genomes]
rs11164848	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11164849	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12092304	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12747275	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4847386	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4847389	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs514235	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs521428	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs606344	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs619784	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs641462	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs660870	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6671078	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6671268	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6681240	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs753391	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs770884	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	esv3339713	chr1:93425789-93428737	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6681345	FAM69A	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93425200-93428000	Active TSS	Brain Hippocampus Middle	brain
2	chr1:93425200-93428000	Active TSS	NHDF-Ad	bronchial
3	chr1:93425200-93428200	Active TSS	Liver	Liver
4	chr1:93425200-93428200	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr1:93425200-93428200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:93425200-93428200	Active TSS	Brain Substantia Nigra	brain
7	chr1:93425400-93428200	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr1:93425400-93428200	Active TSS	Brain Angular Gyrus	brain
9	chr1:93425400-93428200	Active TSS	Brain Anterior Caudate	brain
10	chr1:93425600-93427800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:93425600-93427800	Active TSS	Brain Cingulate Gyrus	brain
12	chr1:93425600-93427800	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr1:93425600-93428000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:93425600-93428000	Active TSS	Fetal Brain Female	brain
15	chr1:93425600-93428000	Active TSS	Pancreas	Pancrea
16	chr1:93425600-93428200	Active TSS	Colonic Mucosa	Colon
17	chr1:93425600-93428200	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr1:93425600-93428400	Active TSS	Aorta	Aorta
19	chr1:93425800-93427600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:93425800-93427600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:93425800-93427800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:93425800-93427800	Active TSS	Fetal Intestine Small	intestine
23	chr1:93425800-93427800	Active TSS	Rectal Smooth Muscle	rectum
24	chr1:93425800-93427800	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr1:93425800-93427800	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr1:93425800-93428000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr1:93425800-93428000	Active TSS	Colon Smooth Muscle	Colon
28	chr1:93425800-93428000	Active TSS	Psoas Muscle	Psoas
29	chr1:93425800-93428000	Active TSS	Right Atrium	heart
30	chr1:93425800-93428000	Active TSS	Right Ventricle	heart
31	chr1:93425800-93428200	Active TSS	GM12878-XiMat	blood
32	chr1:93426000-93427600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:93426000-93427600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr1:93426000-93427600	Active TSS	Fetal Muscle Trunk	muscle
35	chr1:93426000-93427600	Active TSS	NHEK	skin
36	chr1:93426000-93427800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:93426000-93427800	Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr1:93426000-93427800	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr1:93426000-93427800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:93426000-93427800	Active TSS	Esophagus	oesophagus
41	chr1:93426000-93427800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr1:93426000-93427800	Active TSS	Fetal Stomach	stomach
43	chr1:93426000-93427800	Active TSS	Lung	lung
44	chr1:93426000-93427800	Active TSS	Small Intestine	intestine
45	chr1:93426000-93427800	Active TSS	Stomach Mucosa	stomach
46	chr1:93426000-93428000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:93426000-93428000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:93426000-93428000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:93426000-93428000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:93426000-93428000	Active TSS	Fetal Intestine Large	intestine

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