Variant report

Variant	rs34041593
Chromosome Location	chr1:93427662-93427663
allele	A/C
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	POLR2A	chr1:93425826-93428558	GM12878	blood:	n/a	n/a
3	MXI1	chr1:93425637-93427664	HepG2	liver:	n/a	n/a
4	E2F6	chr1:93426133-93427751	K562	blood:	n/a	chr1:93426330-93426339 chr1:93426780-93426789 chr1:93427312-93427324
5	POLR2A	chr1:93425974-93428432	GM18526	blood:	n/a	n/a
6	BHLHE40	chr1:93426942-93428033	K562	blood:	n/a	chr1:93427324-93427340 chr1:93427224-93427240 chr1:93427195-93427211 chr1:93427198-93427214
7	ELK1	chr1:93427294-93427798	GM12878	blood:	n/a	n/a
8	CTCF	chr1:93427580-93427730	GM12872	blood:	n/a	n/a
9	PML	chr1:93425555-93428546	GM12878	blood:	n/a	n/a
10	JUND	chr1:93427135-93427719	K562	blood:	n/a	n/a
11	ZNF384	chr1:93427562-93428441	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:93426925-93427709	GM12878	blood:	n/a	n/a
13	MAZ	chr1:93425647-93428513	IMR90	lung:	n/a	chr1:93427313-93427323 chr1:93428231-93428240
14	CTCF	chr1:93427656-93427664	GM12891	blood:	n/a	n/a
15	POLR2A	chr1:93426663-93427726	MCF-7	breast:	n/a	n/a
16	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
17	MAX	chr1:93425976-93428067	Hela-S3	cervix:	n/a	chr1:93427313-93427323
18	CEBPB	chr1:93427429-93427732	K562	blood:	n/a	chr1:93427540-93427552
19	MAX	chr1:93425879-93428020	A549	lung:	n/a	chr1:93427313-93427323
20	ETS1	chr1:93427127-93427779	GM12878	blood:	n/a	chr1:93427432-93427441
21	EBF1	chr1:93427365-93427760	GM12878	blood:	n/a	chr1:93427572-93427583 chr1:93427573-93427582 chr1:93427571-93427584 chr1:93427573-93427582 chr1:93427573-93427583
22	POLR2A	chr1:93427068-93427748	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:93426795-93428377	MCF10A-Er-Src	breast:	n/a	n/a
24	MAX	chr1:93425890-93427764	ECC-1	luminal epithelium:	n/a	chr1:93427313-93427323
25	ZMIZ1	chr1:93427183-93428110	K562	blood:	n/a	n/a
26	POLR2A	chr1:93426840-93427665	K562	blood:	n/a	n/a
27	ELF1	chr1:93427095-93427847	GM12878	blood:	n/a	chr1:93427197-93427209 chr1:93427310-93427322 chr1:93427429-93427442 chr1:93427330-93427339 chr1:93427309-93427318 chr1:93427431-93427440 chr1:93427260-93427269
28	ATF2	chr1:93427523-93428492	GM12878	blood:	n/a	n/a
29	CCNT2	chr1:93426402-93427760	K562	blood:	n/a	chr1:93426531-93426540 chr1:93426767-93426776
30	POLR2A	chr1:93426739-93428372	ProgFib	skin:	n/a	n/a
31	MAX	chr1:93427064-93427804	H1-hESC	embryonic stem cell:	n/a	chr1:93427313-93427323
32	CHD1	chr1:93427154-93428515	GM12878	blood:	n/a	n/a
33	REST	chr1:93425567-93427894	H1-neurons	neurons:	n/a	chr1:93427438-93427451 chr1:93426707-93426720 chr1:93426707-93426720 chr1:93426761-93426774
34	TCF12	chr1:93427327-93427746	GM12878	blood:	n/a	n/a
35	RELA	chr1:93425928-93428479	GM15510	blood:	n/a	chr1:93426541-93426550 chr1:93426541-93426550
36	POLR2A	chr1:93426792-93427702	K562	blood:	n/a	n/a
37	HMGN3	chr1:93426551-93427986	K562	blood:	n/a	n/a
38	SRF	chr1:93427592-93428422	HCT-116	colon:	n/a	chr1:93427991-93428006 chr1:93427993-93428004 chr1:93427992-93428005 chr1:93427988-93428006 chr1:93427994-93428003 chr1:93427992-93428005 chr1:93427990-93428007 chr1:93427994-93428005 chr1:93427990-93428008
39	POLR2A	chr1:93426740-93427663	ECC-1	luminal epithelium:	n/a	n/a
40	CHD2	chr1:93427641-93428015	Hela-S3	cervix:	n/a	n/a
41	ZBTB7A	chr1:93426007-93427961	ECC-1	luminal epithelium:	n/a	chr1:93427393-93427404 chr1:93427321-93427330
42	POLR2A	chr1:93425557-93428497	GM18505	blood:	n/a	n/a
43	MAX	chr1:93427098-93427676	SK-N-SH	brain:	n/a	chr1:93427313-93427323
44	CTCF	chr1:93427540-93427690	GM12872	blood:	n/a	n/a
45	POLR2A	chr1:93425643-93429210	GM12891	blood:	n/a	n/a
46	RELA	chr1:93425735-93428545	GM12891	blood:	n/a	chr1:93426541-93426550 chr1:93426541-93426550
47	POLR2A	chr1:93425948-93428399	GM19193	blood:	n/a	n/a
48	CTCF	chr1:93427580-93427730	HEK293	kidney:	n/a	n/a
49	POLR2A	chr1:93425928-93428432	GM12878	blood:	n/a	n/a
50	FOXP2	chr1:93427428-93427692	SK-N-MC	brain:	n/a	n/a

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	chr1:93427351..93429788-chr1:93458702..93460989,2	MCF-7	breast:
4	chr1:93296356..93298770-chr1:93426282..93429088,3	MCF-7	breast:
5	chr1:93323615..93326108-chr1:93427081..93429012,3	K562	blood:
6	chr1:93425058..93429733-chr1:93431759..93435608,8	K562	blood:
7	chr1:93323615..93326108-chr1:93427081..93429012,2	K562	blood:

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

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10874745	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11164825	0.83[EUR][1000 genomes]
rs11582791	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11583491	0.86[ASN][1000 genomes]
rs11586089	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11586570	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12062315	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12081675	0.86[ASN][1000 genomes]
rs12082659	0.86[ASN][1000 genomes]
rs12726286	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12728322	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12738654	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12746956	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12750269	0.85[EUR][1000 genomes]
rs1854797	0.83[EUR][1000 genomes]
rs2893226	0.86[ASN][1000 genomes]
rs34098754	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34244251	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35031391	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35051335	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35183060	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35807969	0.86[ASN][1000 genomes]
rs56193705	0.86[ASN][1000 genomes]
rs58270016	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6604026	0.86[ASN][1000 genomes]
rs66525381	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6657809	0.86[ASN][1000 genomes]
rs6687931	0.86[ASN][1000 genomes]
rs71652510	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7514280	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7521417	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7543548	0.86[ASN][1000 genomes]
rs7554594	0.82[EUR][1000 genomes];0.86[ASN][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
rs34041593	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	chr1:93425800-93427800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:93425800-93427800	Active TSS	Fetal Intestine Small	intestine
21	chr1:93425800-93427800	Active TSS	Rectal Smooth Muscle	rectum
22	chr1:93425800-93427800	Active TSS	Sigmoid Colon	Sigmoid Colon
23	chr1:93425800-93427800	Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr1:93425800-93428000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr1:93425800-93428000	Active TSS	Colon Smooth Muscle	Colon
26	chr1:93425800-93428000	Active TSS	Psoas Muscle	Psoas
27	chr1:93425800-93428000	Active TSS	Right Atrium	heart
28	chr1:93425800-93428000	Active TSS	Right Ventricle	heart
29	chr1:93425800-93428200	Active TSS	GM12878-XiMat	blood
30	chr1:93426000-93427800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:93426000-93427800	Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr1:93426000-93427800	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr1:93426000-93427800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:93426000-93427800	Active TSS	Esophagus	oesophagus
35	chr1:93426000-93427800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr1:93426000-93427800	Active TSS	Fetal Stomach	stomach
37	chr1:93426000-93427800	Active TSS	Lung	lung
38	chr1:93426000-93427800	Active TSS	Small Intestine	intestine
39	chr1:93426000-93427800	Active TSS	Stomach Mucosa	stomach
40	chr1:93426000-93428000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:93426000-93428000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:93426000-93428000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:93426000-93428000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:93426000-93428000	Active TSS	Fetal Intestine Large	intestine
45	chr1:93426000-93428000	Active TSS	Left Ventricle	heart
46	chr1:93426000-93428000	Active TSS	Ovary	ovary
47	chr1:93426000-93428000	Active TSS	Thymus	Thymus
48	chr1:93426000-93428000	Active TSS	A549	lung
49	chr1:93426000-93428200	Active TSS	H9 Cell Line	embryonic stem cell
50	chr1:93426000-93428200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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