Variant report

Variant	rs2619680
Chromosome Location	chr15:40988418-40988419
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr15:40988318-40988452	K562	blood:	n/a	n/a
2	MXI1	chr15:40986009-40988732	SK-N-SH	brain:	n/a	n/a
3	GTF3C2	chr15:40986514-40988597	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr15:40988375-40988781	K562	blood:	n/a	n/a
5	GTF3C2	chr15:40987013-40988766	K562	blood:	n/a	n/a
6	MXI1	chr15:40986251-40988507	IMR90	lung:	n/a	n/a
7	HEY1	chr15:40988403-40988821	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40985800..40990095-chr15:41055400..41057901,4	K562	blood:
2	chr15:40987359..40990886-chr15:41044779..41048321,5	K562	blood:
3	chr15:40987273..40988882-chr15:41061961..41063775,2	K562	blood:
4	chr15:40986558..40989601-chr15:40990368..40993764,9	K562	blood:
5	chr15:40860821..40863087-chr15:40987318..40989233,3	K562	blood:
6	chr15:40984748..40990654-chr15:41044779..41050104,8	K562	blood:
7	chr15:40987923..40990095-chr15:41055400..41057842,2	K562	blood:
8	chr15:40986478..40988882-chr15:41036813..41039846,3	K562	blood:

No data

Variant related genes	Relation type
RAD51	TF binding region
RAD51-AS1	TF binding region
ENSG00000104129	Chromatin interaction
ENSG00000188277	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000166133	Chromatin interaction
ENSG00000051180	Chromatin interaction
ENSG00000137880	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10775121	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070291	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070293	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11631563	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11633269	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11852786	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11855560	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11858337	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858338	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12372947	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12439683	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441514	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12442845	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12593359	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12908284	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912742	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2263551	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304582	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2412546	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412547	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412548	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412549	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577564	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2619679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2619683	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2917955	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2928140	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3092982	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3092983	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3101861	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34400306	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36106105	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs45495293	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4923884	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924493	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924495	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4924501	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924503	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56042757	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6492961	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164339	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7167854	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7169010	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7172195	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7173646	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7174551	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7175401	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs752012	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8025883	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8033829	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8036817	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats 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	44 gene(s)	inside rSNPs	diseases
4	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv529030	chr15:40956471-41012695	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv904100	chr15:40959624-40994706	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
10	nsv527234	chr15:40987725-41031686	Transcr. at gene 5' and 3' Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2619680	RP11-111A22.1	cis	lung	GTEx
rs2619680	CCDC32	cis	multi-tissue	Pritchard
rs2619680	RP11-111A22.1	cis	Artery Tibial	GTEx
rs2619680	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs2619680	RAD51	cis	multi-tissue	Pritchard
rs2619680	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs2619680	C15orf57	cis	lung	GTEx
rs2619680	C15orf57	cis	Adipose Subcutaneous	GTEx
rs2619680	C15orf57	cis	Nerve Tibial	GTEx
rs2619680	C15orf57	cis	Artery Tibial	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40986000-40988600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr15:40986000-40988600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:40986000-40988600	Active TSS	NH-A	brain
4	chr15:40986000-40988800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:40986000-40989000	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr15:40986000-40989200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:40986200-40988600	Active TSS	H1 Cell Line	embryonic stem cell
8	chr15:40986200-40988600	Active TSS	H9 Cell Line	embryonic stem cell
9	chr15:40986200-40988800	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr15:40986200-40988800	Active TSS	Fetal Kidney	kidney
11	chr15:40986200-40989000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:40986200-40989000	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr15:40986200-40989000	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr15:40986200-40989200	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr15:40986400-40988600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:40986400-40988600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:40986400-40988600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:40986400-40988600	Active TSS	A549	lung
19	chr15:40986400-40988800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr15:40986400-40988800	Active TSS	HSMM	muscle
21	chr15:40986400-40988800	Active TSS	NHLF	lung
22	chr15:40986400-40989200	Active TSS	K562	blood
23	chr15:40986600-40988600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:40986600-40988600	Active TSS	Fetal Brain Female	brain
25	chr15:40986600-40989200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr15:40986600-40989200	Active TSS	HMEC	breast
27	chr15:40986800-40988600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:40986800-40988600	Active TSS	Duodenum Mucosa	Duodenum
29	chr15:40987000-40988600	Active TSS	Fetal Intestine Small	intestine
30	chr15:40987600-40988800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:40987600-40988800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr15:40987800-40988600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr15:40987800-40988600	Active TSS	Gastric	stomach
34	chr15:40987800-40988800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr15:40987800-40993600	Weak transcription	Lung	lung
36	chr15:40988000-40988600	Active TSS	Brain Germinal Matrix	brain
37	chr15:40988000-40988800	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr15:40988000-40991600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr15:40988000-40999400	Weak transcription	Right Atrium	heart
40	chr15:40988000-41030000	Weak transcription	Pancreas	Pancrea
41	chr15:40988200-40988600	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr15:40988200-40988600	Enhancers	Primary T cells fromperipheralblood	blood
43	chr15:40988200-40988600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:40988200-40988600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr15:40988200-40988600	Enhancers	Adipose Nuclei	Adipose
46	chr15:40988200-40988600	Active TSS	Fetal Stomach	stomach
47	chr15:40988200-40988800	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr15:40988200-40988800	Enhancers	Primary T cells from cord blood	blood
49	chr15:40988200-40988800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr15:40988200-40988800	Enhancers	Rectal Mucosa Donor 31	rectum

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