Variant report

Variant	rs1008979
Chromosome Location	chr15:42399642-42399643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42398541..42400541-chr15:42411116..42413868,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1008781	0.92[ASN][1000 genomes]
rs1008782	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11629612	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs11630163	0.83[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11638728	0.92[CHB][hapmap];0.90[CHD][hapmap];0.87[ASN][1000 genomes]
rs12050606	0.92[ASN][1000 genomes]
rs2167295	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8042630	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv457121	chr15:42396282-42418085	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv569236	chr15:42396282-42418085	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1008979	RTF1	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42393000-42399800	Weak transcription	Right Atrium	heart
2	chr15:42394600-42400200	Enhancers	Fetal Thymus	thymus
3	chr15:42395200-42404000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr15:42395400-42400600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:42396200-42404200	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr15:42396200-42405200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr15:42397400-42400200	Enhancers	Brain Germinal Matrix	brain
8	chr15:42397600-42400000	Enhancers	Fetal Muscle Trunk	muscle
9	chr15:42397600-42400000	Enhancers	GM12878-XiMat	blood
10	chr15:42397600-42400200	Enhancers	Fetal Muscle Leg	muscle
11	chr15:42397800-42399800	Weak transcription	Fetal Intestine Small	intestine
12	chr15:42397800-42402200	Weak transcription	Dnd41	blood
13	chr15:42398000-42400800	Bivalent Enhancer	HepG2	liver
14	chr15:42398200-42400000	Enhancers	Stomach Mucosa	stomach
15	chr15:42398800-42400000	Enhancers	Lung	lung
16	chr15:42399000-42400200	Enhancers	Fetal Brain Male	brain
17	chr15:42399000-42400800	Enhancers	Gastric	stomach
18	chr15:42399200-42399800	Weak transcription	Esophagus	oesophagus
19	chr15:42399200-42400400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr15:42399600-42399800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:42399600-42399800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr15:42399600-42399800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:42399600-42399800	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr15:42399600-42399800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr15:42399600-42399800	Bivalent Enhancer	HSMM	muscle
26	chr15:42399600-42399800	Flanking Bivalent TSS/Enh	NH-A	brain
27	chr15:42399600-42400000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr15:42399600-42400000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:42399600-42400000	Flanking Active TSS	Brain Angular Gyrus	brain
30	chr15:42399600-42400000	Active TSS	Brain Anterior Caudate	brain
31	chr15:42399600-42400000	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr15:42399600-42400000	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr15:42399600-42400000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
34	chr15:42399600-42400000	Flanking Active TSS	Fetal Brain Female	brain
35	chr15:42399600-42400000	Enhancers	Pancreas	Pancrea
36	chr15:42399600-42400000	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr15:42399600-42400000	Enhancers	Thymus	Thymus
38	chr15:42399600-42400000	Flanking Active TSS	NHEK	skin
39	chr15:42399600-42400400	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr15:42399600-42400600	Enhancers	HMEC	breast
41	chr15:42399600-42400800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:42399600-42400800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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