Variant report

Variant	rs2815408
Chromosome Location	chr1:93646620-93646621
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	TCF12	chr1:93645255-93646997	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr1:93644995-93646951	PFSK-1	brain:	n/a	n/a
3	SIN3AK20	chr1:93645308-93646661	PANC-1	pancreas:	n/a	n/a
4	ZNF384	chr1:93645246-93647334	K562	blood:	n/a	n/a
5	NFATC1	chr1:93646284-93647009	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:93645090-93646896	Hela-S3	cervix:	n/a	n/a
7	MAX	chr1:93645075-93646831	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:93645008-93647230	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr1:93645158-93647047	Raji	blood:	n/a	n/a
10	PML	chr1:93644916-93647169	K562	blood:	n/a	n/a
11	POLR2A	chr1:93645286-93647098	K562	blood:	n/a	n/a
12	CHD1	chr1:93644469-93647061	GM12878	blood:	n/a	chr1:93645456-93645466
13	SPI1	chr1:93645667-93646974	HL-60	blood:	n/a	chr1:93646742-93646751
14	POLR2A	chr1:93645155-93647101	HL-60	blood:	n/a	n/a
15	MAX	chr1:93645210-93646711	HUVEC	blood vessel:	n/a	n/a
16	MAX	chr1:93644987-93647107	GM12878	blood:	n/a	n/a
17	CBX3	chr1:93645030-93647181	K562	blood:	n/a	n/a
18	RUNX3	chr1:93644998-93646823	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:93645046-93647124	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:93645337-93647074	K562	blood:	n/a	n/a
21	YY1	chr1:93645704-93646916	GM12878	blood:	n/a	chr1:93646761-93646770 chr1:93646758-93646769
22	PML	chr1:93645059-93647177	K562	blood:	n/a	n/a
23	EGR1	chr1:93646447-93647027	K562	blood:	n/a	chr1:93646761-93646775 chr1:93646763-93646773 chr1:93646757-93646766 chr1:93646762-93646775 chr1:93646762-93646772 chr1:93646760-93646770 chr1:93646762-93646775 chr1:93646756-93646769 chr1:93646761-93646776 chr1:93646762-93646775 chr1:93646762-93646775 chr1:93646757-93646779 chr1:93646763-93646772 chr1:93646763-93646774 chr1:93646759-93646773
24	SIN3AK20	chr1:93645385-93646743	MCF-7	breast:	n/a	n/a
25	POLR2A	chr1:93645216-93646684	HepG2	liver:	n/a	n/a
26	TCF7L2	chr1:93645248-93646691	Hela-S3	cervix:	n/a	n/a
27	E2F6	chr1:93645169-93646829	H1-hESC	embryonic stem cell:	n/a	chr1:93645464-93645473 chr1:93646761-93646770 chr1:93645701-93645712
28	ETS1	chr1:93646493-93646968	GM12878	blood:	n/a	chr1:93646761-93646772
29	POLR2A	chr1:93645166-93647028	GM18951	blood:	n/a	n/a
30	YY1	chr1:93645290-93646838	K562	blood:	n/a	chr1:93646761-93646770 chr1:93646758-93646769
31	ATF1	chr1:93645868-93647025	K562	blood:	n/a	n/a
32	ELK1	chr1:93645216-93647028	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr1:93645226-93647161	K562	blood:	n/a	n/a
34	YY1	chr1:93645741-93646872	SK-N-SH	brain:	n/a	chr1:93646761-93646770 chr1:93646758-93646769
35	GATA1	chr1:93644434-93647154	PBDE	blood:	n/a	n/a
36	POLR2A	chr1:93645197-93647070	GM15510	blood:	n/a	n/a
37	POLR2A	chr1:93645225-93646658	HEK293	kidney:	n/a	n/a
38	MXI1	chr1:93645091-93646690	HepG2	liver:	n/a	n/a
39	CREB1	chr1:93645443-93646652	K562	blood:	n/a	n/a
40	GABPA	chr1:93645417-93646823	K562	blood:	n/a	chr1:93646761-93646770 chr1:93645463-93645474 chr1:93645463-93645477 chr1:93645460-93645474 chr1:93645465-93645474
41	TBL1XR1	chr1:93645025-93647145	K562	blood:	n/a	n/a
42	NFIC	chr1:93644930-93647114	GM12878	blood:	n/a	chr1:93645104-93645121
43	RCOR1	chr1:93645014-93647057	K562	blood:	n/a	n/a
44	POLR2A	chr1:93644987-93647172	GM12878	blood:	n/a	n/a
45	YY1	chr1:93645851-93646839	GM12891	blood:	n/a	chr1:93646761-93646770 chr1:93646758-93646769
46	MXI1	chr1:93645510-93646692	H1-hESC	embryonic stem cell:	n/a	n/a
47	YY1	chr1:93645846-93646835	ECC-1	luminal epithelium:	n/a	chr1:93646761-93646770 chr1:93646758-93646769
48	PML	chr1:93644875-93647216	GM12878	blood:	n/a	n/a
49	POLR2A	chr1:93645076-93647191	GM12892	blood:	n/a	n/a
50	E2F6	chr1:93645307-93646710	H1-hESC	embryonic stem cell:	n/a	chr1:93645464-93645473 chr1:93645701-93645712

No.	Distal block	Cell Line	Cell type
1	chr1:93645541..93647091-chr1:93656418..93658733,2	K562	blood:
2	chr1:93646436..93648655-chr1:93649128..93651359,3	MCF-7	breast:
3	chr1:93543004..93547095-chr1:93643826..93649088,10	K562	blood:
4	chr1:93645225..93647960-chr1:93665324..93667847,2	MCF-7	breast:
5	chr1:93645217..93647483-chr1:93810016..93813905,4	K562	blood:
6	chr1:93543004..93547588-chr1:93644888..93649088,6	K562	blood:
7	chr1:93646277..93649734-chr1:93664673..93670683,6	K562	blood:
8	chr1:93645897..93646803-chr9:91926043..91926625,2	Hela-S3	cervix:
9	chr1:93644831..93648972-chr1:93800687..93805034,4	K562	blood:
10	chr1:93296314..93299115-chr1:93644282..93648010,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMED5-3	chr1:93646483-93646717	NONHSAT004485

Variant related genes	Relation type
TMED5	TF binding region
ENSG00000225297	Chromatin interaction
ENSG00000117505	Chromatin interaction
ENSG00000143033	Chromatin interaction
ENSG00000123975	Chromatin interaction
ENSG00000237003	Chromatin interaction
ENSG00000223745	Chromatin interaction
ENSG00000122406	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10782958	0.81[EUR][1000 genomes]
rs1081526	0.87[AMR][1000 genomes]
rs10874765	0.81[EUR][1000 genomes]
rs10874767	0.80[EUR][1000 genomes]
rs10874771	0.81[EUR][1000 genomes]
rs11164874	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11164878	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11164882	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11164888	0.80[EUR][1000 genomes]
rs11164889	0.80[EUR][1000 genomes]
rs11164890	0.80[EUR][1000 genomes]
rs11582703	0.81[EUR][1000 genomes]
rs11586323	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12057476	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12064785	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12066315	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12067005	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12070900	0.81[EUR][1000 genomes]
rs12071627	0.81[EUR][1000 genomes]
rs12080715	0.80[EUR][1000 genomes]
rs12085959	0.81[EUR][1000 genomes]
rs12087466	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12088338	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12090723	0.81[EUR][1000 genomes]
rs12094547	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12731675	0.81[EUR][1000 genomes]
rs12731809	0.81[EUR][1000 genomes]
rs1323626	0.87[AMR][1000 genomes]
rs1323628	0.84[AMR][1000 genomes]
rs1414367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1535698	0.81[EUR][1000 genomes]
rs17131699	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2391227	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2484485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2749735	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2783492	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2783498	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2783506	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2815409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2815410	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2815411	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2815412	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2815413	0.92[EUR][1000 genomes]
rs2815414	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36057148	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4573531	0.81[EUR][1000 genomes]
rs485622	0.85[EUR][1000 genomes]
rs504810	0.82[EUR][1000 genomes]
rs505531	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs506556	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs519723	0.84[EUR][1000 genomes]
rs522999	0.92[EUR][1000 genomes]
rs546	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55701931	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs559397	0.81[EUR][1000 genomes]
rs56303209	0.81[EUR][1000 genomes]
rs566743	0.81[EUR][1000 genomes]
rs571212	0.84[EUR][1000 genomes]
rs573056	0.89[EUR][1000 genomes]
rs581825	0.91[EUR][1000 genomes]
rs587754	0.81[EUR][1000 genomes]
rs605759	0.86[EUR][1000 genomes]
rs615416	0.92[EUR][1000 genomes]
rs626714	0.80[EUR][1000 genomes]
rs629153	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs637198	0.80[EUR][1000 genomes]
rs658178	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs658877	0.92[EUR][1000 genomes]
rs661566	0.83[EUR][1000 genomes]
rs662546	0.83[EUR][1000 genomes]
rs6657587	0.80[EUR][1000 genomes]
rs6667701	0.80[EUR][1000 genomes]
rs667680	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs670650	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs671559	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs693872	0.82[EUR][1000 genomes]
rs698926	0.87[AMR][1000 genomes]
rs71510760	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7551635	0.81[EUR][1000 genomes]
rs7555292	0.81[EUR][1000 genomes]
rs771452	0.87[AMR][1000 genomes]
rs771457	0.87[AMR][1000 genomes]
rs771460	0.87[AMR][1000 genomes]
rs771464	0.81[AMR][1000 genomes]
rs771466	0.87[AMR][1000 genomes]
rs771472	0.87[AMR][1000 genomes]
rs771474	0.87[AMR][1000 genomes]
rs771480	0.87[AMR][1000 genomes]
rs797660	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs797669	0.82[EUR][1000 genomes]
rs809515	0.84[EUR][1000 genomes]
rs9432700	0.81[EUR][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	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2815408	RP4-717I23.3	cis	Stomach	GTEx
rs2815408	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs2815408	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs2815408	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs2815408	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs2815408	RP4-717I23.3	cis	Artery Tibial	GTEx
rs2815408	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs2815408	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2815408	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs2815408	RP4-717I23.3	cis	lung	GTEx
rs2815408	RP4-717I23.3	cis	Whole Blood	GTEx
rs2815408	RP4-717I23.3	cis	Artery Aorta	GTEx
rs2815408	RP4-717I23.3	cis	Thyroid	GTEx
rs2815408	RP4-717I23.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93642000-93647000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:93642200-93646800	Active TSS	Hela-S3	cervix
3	chr1:93642200-93647200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:93642400-93646800	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr1:93642600-93647800	Active TSS	K562	blood
6	chr1:93642800-93647000	Active TSS	Psoas Muscle	Psoas
7	chr1:93642800-93647200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr1:93643000-93647000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:93643000-93647600	Active TSS	NHLF	lung
10	chr1:93643000-93648400	Active TSS	GM12878-XiMat	blood
11	chr1:93643200-93647000	Active TSS	NHDF-Ad	bronchial
12	chr1:93643200-93647400	Active TSS	A549	lung
13	chr1:93643200-93647600	Active TSS	HMEC	breast
14	chr1:93643400-93646800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:93643400-93646800	Active TSS	Stomach Smooth Muscle	stomach
16	chr1:93643400-93647200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:93643600-93647200	Active TSS	H1 Cell Line	embryonic stem cell
18	chr1:93643600-93647200	Active TSS	H9 Cell Line	embryonic stem cell
19	chr1:93643600-93647400	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr1:93643600-93647600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:93643600-93647800	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr1:93643800-93646800	Active TSS	Right Ventricle	heart
23	chr1:93643800-93647000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr1:93643800-93647000	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr1:93643800-93647200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:93643800-93647200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:93643800-93647200	Active TSS	Colonic Mucosa	Colon
28	chr1:93644000-93646800	Active TSS	Brain Angular Gyrus	brain
29	chr1:93644000-93646800	Active TSS	NH-A	brain
30	chr1:93644000-93647800	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr1:93644200-93646800	Active TSS	Muscle Satellite Cultured Cells	--
32	chr1:93644200-93646800	Active TSS	Brain Cingulate Gyrus	brain
33	chr1:93644200-93646800	Active TSS	Fetal Brain Female	brain
34	chr1:93644200-93646800	Active TSS	Fetal Thymus	thymus
35	chr1:93644200-93646800	Active TSS	Left Ventricle	heart
36	chr1:93644200-93646800	Active TSS	NHEK	skin
37	chr1:93644200-93647000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:93644200-93647000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:93644200-93647000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:93644200-93647000	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr1:93644200-93647200	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr1:93644200-93647200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr1:93644200-93647200	Active TSS	Fetal Intestine Large	intestine
44	chr1:93644200-93647200	Active TSS	Fetal Kidney	kidney
45	chr1:93644200-93647200	Active TSS	HSMMtube	muscle
46	chr1:93644200-93648000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:93644400-93646800	Active TSS	Fetal Stomach	stomach
48	chr1:93644400-93646800	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr1:93644400-93646800	Active TSS	HSMM	muscle
50	chr1:93644400-93647200	Active TSS	Brain Anterior Caudate	brain

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