Variant report

Variant	rs2505512
Chromosome Location	chr10:43633596-43633597
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	YY1	chr10:43633145-43634070	GM12878	blood:	n/a	chr10:43633628-43633639 chr10:43633628-43633637 chr10:43633935-43633944 chr10:43633589-43633598 chr10:43633932-43633941 chr10:43633623-43633637
2	ZNF263	chr10:43633091-43634745	HEK293-T-REx	kidney:	n/a	n/a
3	POLR2A	chr10:43632606-43634349	MCF-7	breast:	n/a	n/a
4	POLR2A	chr10:43633535-43634144	U87	brain:	n/a	n/a
5	MAZ	chr10:43632957-43634841	IMR90	lung:	n/a	n/a
6	MAX	chr10:43632952-43634463	A549	lung:	n/a	n/a
7	MAX	chr10:43633060-43634074	A549	lung:	n/a	n/a
8	POLR2A	chr10:43633440-43634432	GM12878	blood:	n/a	n/a
9	TAF1	chr10:43633589-43634131	ECC-1	luminal epithelium:	n/a	n/a
10	CTBP2	chr10:43633047-43634578	H1-hESC	embryonic stem cell:	n/a	n/a
11	TBP	chr10:43633414-43634183	GM12878	blood:	n/a	n/a
12	CREB1	chr10:43633052-43634165	HepG2	liver:	n/a	n/a
13	POLR2A	chr10:43633218-43634781	MCF10A-Er-Src	breast:	n/a	n/a
14	PAX5	chr10:43633476-43633750	GM12892	blood:	n/a	n/a
15	ETS1	chr10:43633523-43634137	K562	blood:	n/a	chr10:43633874-43633890 chr10:43633881-43633890 chr10:43633879-43633888 chr10:43633930-43633941 chr10:43633878-43633891 chr10:43633881-43633890 chr10:43633882-43633892 chr10:43633881-43633890 chr10:43633881-43633890 chr10:43633881-43633890 chr10:43633881-43633892
16	UBTF	chr10:43633282-43634588	K562	blood:	n/a	n/a
17	NRF1	chr10:43633510-43634154	GM12878	blood:	n/a	n/a
18	POLR2A	chr10:43633139-43634242	GM12878	blood:	n/a	n/a
19	POLR2A	chr10:43632951-43634291	MCF-7	breast:	n/a	n/a
20	MTA3	chr10:43632911-43633719	GM12878	blood:	n/a	n/a
21	CTCF	chr10:43633560-43633710	NHEK	skin:	n/a	n/a
22	YY1	chr10:43632919-43634147	SK-N-SH_RA	brain:	n/a	chr10:43633628-43633639 chr10:43633040-43633054 chr10:43633628-43633637 chr10:43633935-43633944 chr10:43633589-43633598 chr10:43633932-43633941 chr10:43633623-43633637
23	SIN3A	chr10:43632962-43634559	H1-hESC	embryonic stem cell:	n/a	chr10:43634346-43634357 chr10:43633042-43633051 chr10:43633177-43633188
24	REST	chr10:43633504-43634017	PFSK-1	brain:	n/a	chr10:43633670-43633679 chr10:43633672-43633679 chr10:43633984-43633997
25	POLR2A	chr10:43633101-43634321	HUVEC	blood vessel:	n/a	n/a
26	REST	chr10:43632910-43634056	U87	brain:	n/a	chr10:43633670-43633679 chr10:43633672-43633679 chr10:43632957-43632970 chr10:43633984-43633997
27	ELF1	chr10:43633527-43634201	GM12878	blood:	n/a	chr10:43633927-43633939 chr10:43633932-43633941 chr10:43633933-43633945 chr10:43633877-43633890
28	TAF1	chr10:43633559-43634147	HepG2	liver:	n/a	n/a
29	RCOR1	chr10:43633163-43634720	K562	blood:	n/a	n/a
30	POLR2A	chr10:43633174-43634586	GM15510	blood:	n/a	n/a
31	CTCF	chr10:43633501-43633620	MCF-7	breast:	n/a	n/a
32	MAX	chr10:43633147-43634180	MCF-7	breast:	n/a	n/a
33	ZC3H11A	chr10:43633489-43633870	K562	blood:	n/a	n/a
34	POLR2A	chr10:43633145-43634231	GM12878	blood:	n/a	n/a
35	CREB1	chr10:43633079-43634221	A549	lung:	n/a	n/a
36	ETS1	chr10:43633468-43634253	K562	blood:	n/a	chr10:43633874-43633890 chr10:43633881-43633890 chr10:43633879-43633888 chr10:43633930-43633941 chr10:43633878-43633891 chr10:43633881-43633890 chr10:43633882-43633892 chr10:43633881-43633890 chr10:43633881-43633890 chr10:43633881-43633890 chr10:43633881-43633892
37	RELA	chr10:43633350-43634658	GM18951	blood:	n/a	n/a
38	POLR2A	chr10:43632954-43634091	U87	brain:	n/a	n/a
39	CTCF	chr10:43633540-43633690	GM12865	blood:	n/a	n/a
40	POLR2A	chr10:43633571-43634198	Hela-S3	cervix:	n/a	n/a
41	HMGN3	chr10:43633157-43634440	K562	blood:	n/a	n/a
42	POLR2A	chr10:43633340-43634672	GM12878	blood:	n/a	n/a
43	TCF12	chr10:43633077-43633924	A549	lung:	n/a	n/a
44	YY1	chr10:43633117-43634146	GM12892	blood:	n/a	chr10:43633628-43633639 chr10:43633628-43633637 chr10:43633935-43633944 chr10:43633589-43633598 chr10:43633932-43633941 chr10:43633623-43633637
45	SIN3AK20	chr10:43633594-43634082	K562	blood:	n/a	n/a
46	HDAC2	chr10:43633526-43634124	HepG2	liver:	n/a	n/a
47	GABPA	chr10:43633461-43634210	MCF-7	breast:	n/a	n/a
48	POLR2A	chr10:43633104-43634258	Gliobla	brain:	n/a	n/a
49	POLR2A	chr10:43633148-43634187	HepG2	liver:	n/a	n/a
50	POLR2A	chr10:43633197-43634710	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:43631900..43633716-chr10:43902269..43904136,2	MCF-7	breast:
2	chr10:43632409..43636039-chr10:43698014..43700588,4	K562	blood:
3	chr10:43522082..43523941-chr10:43632029..43633686,2	MCF-7	breast:
4	chr10:43633206..43635379-chr10:43761035..43762686,2	MCF-7	breast:
5	chr10:43632694..43635237-chr10:43697053..43700182,3	MCF-7	breast:
6	chr10:43632409..43636039-chr10:43698014..43700588,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RASGEF1A-2	chr10:43632272-43633782	ENSG00000273008.1

Variant related genes	Relation type
CSGALNACT2	TF binding region
ENSG00000198915	Chromatin interaction
ENSG00000169813	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1059484	0.84[ASN][1000 genomes]
rs10793422	0.81[ASN][1000 genomes]
rs1254958	0.82[ASN][1000 genomes]
rs1254959	0.83[ASN][1000 genomes]
rs1254960	0.84[ASN][1000 genomes]
rs1254962	0.84[ASN][1000 genomes]
rs1254963	0.84[ASN][1000 genomes]
rs1254965	0.84[ASN][1000 genomes]
rs1254967	0.84[ASN][1000 genomes]
rs1254968	0.84[ASN][1000 genomes]
rs1270015	0.84[ASN][1000 genomes]
rs1272142	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1800861	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1864395	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1864399	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1864400	0.87[ASN][1000 genomes]
rs2003317	0.84[ASN][1000 genomes]
rs2075910	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2075912	0.90[ASN][1000 genomes]
rs2075913	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2115817	0.84[ASN][1000 genomes]
rs2249005	0.92[ASN][1000 genomes]
rs2257767	0.85[ASN][1000 genomes]
rs2293020	0.84[ASN][1000 genomes]
rs2435337	0.85[ASN][1000 genomes]
rs2435338	0.89[ASN][1000 genomes]
rs2435339	0.89[ASN][1000 genomes]
rs2435354	0.85[ASN][1000 genomes]
rs2435376	0.81[ASN][1000 genomes]
rs2435377	0.84[ASN][1000 genomes]
rs2435383	0.84[ASN][1000 genomes]
rs2435384	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2435385	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2503841	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2503848	0.84[ASN][1000 genomes]
rs2503849	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2503860	0.84[ASN][1000 genomes]
rs2503863	0.84[ASN][1000 genomes]
rs2503864	0.84[ASN][1000 genomes]
rs2503865	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2503866	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2503881	0.84[ASN][1000 genomes]
rs2505505	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2505506	0.87[ASN][1000 genomes]
rs2505511	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2505513	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2505514	0.92[ASN][1000 genomes]
rs2505553	0.84[ASN][1000 genomes]
rs2505554	0.85[AMR][1000 genomes]
rs2505557	0.83[ASN][1000 genomes]
rs2565200	0.90[ASN][1000 genomes]
rs2565201	0.90[ASN][1000 genomes]
rs2742233	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2742234	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2742235	0.85[ASN][1000 genomes]
rs2742237	0.90[ASN][1000 genomes]
rs2742239	0.90[ASN][1000 genomes]
rs2742240	0.92[ASN][1000 genomes]
rs2742241	0.92[ASN][1000 genomes]
rs3004211	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3004214	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs715106	0.88[ASN][1000 genomes]
rs741968	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv1038102	chr10:43441601-43642908	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv895082	chr10:43530071-43755506	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv895083	chr10:43549708-43765485	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1051701	chr10:43555542-43642895	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1046892	chr10:43609488-43636278	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv1042310	chr10:43623060-43688505	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2505512	CSGALNACT2	cis	Artery Tibial	GTEx
rs2505512	CSGALNACT2	cis	Thyroid	GTEx
rs2505512	CSGALNACT2	cis	Esophagus Muscularis	GTEx
rs2505512	CSGALNACT2	cis	Skin Sun Exposed Lower leg	GTEx
rs2505512	CSGALNACT2	cis	Heart Left Ventricle	GTEx
rs2505512	CSGALNACT2	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43632000-43634800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr10:43632000-43635200	Active TSS	HSMM	muscle
3	chr10:43632200-43635000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr10:43632200-43635600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr10:43632200-43635600	Active TSS	HSMMtube	muscle
6	chr10:43632400-43633600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr10:43632400-43635000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr10:43632400-43635000	Active TSS	NHDF-Ad	bronchial
9	chr10:43632600-43633800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:43632600-43633800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr10:43632600-43633800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr10:43632600-43634800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr10:43632600-43634800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr10:43632600-43634800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr10:43632600-43634800	Active TSS	Ovary	ovary
16	chr10:43632600-43634800	Active TSS	NHEK	skin
17	chr10:43632600-43635000	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr10:43632600-43635000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr10:43632600-43635000	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr10:43632600-43635000	Active TSS	Fetal Kidney	kidney
21	chr10:43632600-43635000	Active TSS	Psoas Muscle	Psoas
22	chr10:43632600-43635000	Active TSS	NH-A	brain
23	chr10:43632600-43635200	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr10:43632600-43635200	Active TSS	Brain Angular Gyrus	brain
25	chr10:43632600-43635400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr10:43632600-43635400	Active TSS	Right Atrium	heart
27	chr10:43632600-43635600	Active TSS	Rectal Smooth Muscle	rectum
28	chr10:43632600-43635600	Active TSS	NHLF	lung
29	chr10:43632600-43636200	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr10:43632800-43633600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr10:43632800-43633600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
32	chr10:43632800-43633600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr10:43632800-43633600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr10:43632800-43633600	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr10:43632800-43633600	Flanking Active TSS	Colonic Mucosa	Colon
36	chr10:43632800-43633600	Active TSS	Fetal Brain Male	brain
37	chr10:43632800-43633600	Flanking Active TSS	Placenta	Placenta
38	chr10:43632800-43633800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr10:43632800-43634400	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr10:43632800-43634400	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr10:43632800-43634400	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr10:43632800-43634600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr10:43632800-43634600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr10:43632800-43634600	Active TSS	Colon Smooth Muscle	Colon
45	chr10:43632800-43634600	Active TSS	Fetal Intestine Large	intestine
46	chr10:43632800-43634600	Active TSS	Fetal Intestine Small	intestine
47	chr10:43632800-43634600	Active TSS	Placenta Amnion	Placenta Amnion
48	chr10:43632800-43634800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr10:43632800-43634800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr10:43632800-43634800	Active TSS	H9 Cell Line	embryonic stem cell

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