Variant report

Variant	rs28405635
Chromosome Location	chr15:40605642-40605643
allele	A/G
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	NFIC	chr15:40605595-40606141	SK-N-SH	brain:	n/a	n/a
2	NFIC	chr15:40605550-40606247	ECC-1	luminal epithelium:	n/a	n/a
3	NFIC	chr15:40605637-40606239	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40597155..40599934-chr15:40605080..40607975,2	K562	blood:
2	chr15:40596629..40600129-chr15:40604012..40607975,4	K562	blood:

Variant related genes	Relation type
ENSG00000244705	TF binding region
ENSG00000137841	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12440659	0.81[AMR][1000 genomes]
rs12441303	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412511	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	esv1850798	chr15:40560607-40622191	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv457118	chr15:40565705-40606484	Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv569227	chr15:40565705-40606484	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv827305	chr15:40596162-40625922	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv984054	chr15:40603452-40612578	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28405635	CCDC32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40584200-40614800	Weak transcription	Gastric	stomach
2	chr15:40600000-40614600	Weak transcription	Brain Substantia Nigra	brain
3	chr15:40601200-40605800	Weak transcription	HUVEC	blood vessel
4	chr15:40601200-40612800	Weak transcription	Right Ventricle	heart
5	chr15:40601400-40606400	Weak transcription	Esophagus	oesophagus
6	chr15:40602000-40612600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:40602000-40613000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:40602000-40614600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:40602200-40612600	Weak transcription	Spleen	Spleen
10	chr15:40602400-40605800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:40602400-40605800	Weak transcription	Fetal Brain Male	brain
12	chr15:40602600-40605800	Weak transcription	Hela-S3	cervix
13	chr15:40602600-40606000	Weak transcription	Primary B cells from cord blood	blood
14	chr15:40602600-40606000	Weak transcription	Fetal Thymus	thymus
15	chr15:40602600-40614600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:40602800-40605800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr15:40602800-40606000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr15:40604600-40607400	Enhancers	Pancreas	Pancrea
19	chr15:40604600-40607800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:40604600-40608000	Enhancers	Primary T cells fromperipheralblood	blood
21	chr15:40605000-40607800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr15:40605200-40606000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:40605200-40606600	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr15:40605200-40607400	Enhancers	Fetal Heart	heart
25	chr15:40605200-40607800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:40605400-40606000	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr15:40605400-40606800	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr15:40605400-40608000	Enhancers	Primary hematopoietic stem cells	blood
29	chr15:40605600-40605800	Bivalent Enhancer	NHDF-Ad	bronchial
30	chr15:40605600-40606200	Enhancers	K562	blood
31	chr15:40605600-40606400	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr15:40605600-40606400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr15:40605600-40606400	Enhancers	Right Atrium	heart
34	chr15:40605600-40606600	Enhancers	Primary B cells from peripheral blood	blood
35	chr15:40605600-40606600	Enhancers	Primary T cells from cord blood	blood
36	chr15:40605600-40606600	Enhancers	Colonic Mucosa	Colon
37	chr15:40605600-40606600	Enhancers	Lung	lung
38	chr15:40605600-40606800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr15:40605600-40606800	Enhancers	Dnd41	blood
40	chr15:40605600-40607200	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr15:40605600-40607200	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr15:40605600-40607400	Enhancers	Thymus	Thymus
43	chr15:40605600-40607600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:40605600-40607600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:40605600-40607800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:40605600-40607800	Enhancers	HMEC	breast
47	chr15:40605600-40608000	Enhancers	HSMM	muscle
48	chr15:40605600-40608200	Enhancers	Osteobl	bone

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