Variant report

Variant	rs2292688
Chromosome Location	chr12:104136316-104136317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104134942..104137078-chr12:104139812..104142244,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11608250	0.90[LWK][hapmap]
rs11610831	0.90[LWK][hapmap]
rs4981038	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[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	nsv899479	chr12:104092996-104138918	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv899484	chr12:104118587-104139034	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv899485	chr12:104118587-104143082	Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv899486	chr12:104118587-104170474	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv899488	chr12:104123543-104140517	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2292688	SCYL2	cis	parietal	SCAN
rs2292688	CCDC53	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104125200-104138800	Weak transcription	Aorta	Aorta
2	chr12:104128400-104138800	Weak transcription	Spleen	Spleen
3	chr12:104135600-104136400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr12:104135800-104136400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:104135800-104136600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:104135800-104136800	Enhancers	Fetal Heart	heart
7	chr12:104135800-104137200	Enhancers	Fetal Intestine Large	intestine
8	chr12:104136000-104136400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:104136000-104136400	Enhancers	Liver	Liver
10	chr12:104136000-104136400	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr12:104136000-104136400	Enhancers	Fetal Brain Male	brain
12	chr12:104136000-104136400	Enhancers	Gastric	stomach
13	chr12:104136000-104136400	Enhancers	Left Ventricle	heart
14	chr12:104136000-104136400	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr12:104136000-104136400	Enhancers	Right Atrium	heart
16	chr12:104136000-104136400	Enhancers	Right Ventricle	heart
17	chr12:104136000-104136400	Enhancers	Stomach Mucosa	stomach
18	chr12:104136000-104136600	Enhancers	Brain Germinal Matrix	brain
19	chr12:104136000-104136600	Enhancers	Small Intestine	intestine
20	chr12:104136000-104136600	Flanking Active TSS	NHEK	skin
21	chr12:104136000-104136800	Enhancers	Fetal Brain Female	brain
22	chr12:104136000-104136800	Enhancers	Fetal Intestine Small	intestine
23	chr12:104136000-104136800	Enhancers	A549	lung
24	chr12:104136200-104136400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:104136200-104136400	Active TSS	Brain Anterior Caudate	brain
26	chr12:104136200-104136400	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr12:104136200-104136400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
28	chr12:104136200-104136400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr12:104136200-104136400	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr12:104136200-104136400	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr12:104136200-104136400	Flanking Active TSS	NHDF-Ad	bronchial
32	chr12:104136200-104136600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr12:104136200-104136600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:104136200-104136600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:104136200-104136600	Active TSS	Brain Hippocampus Middle	brain
36	chr12:104136200-104136600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:104136200-104136600	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr12:104136200-104136600	Enhancers	Fetal Muscle Leg	muscle
39	chr12:104136200-104136600	Enhancers	Ovary	ovary
40	chr12:104136200-104136600	Flanking Active TSS	HMEC	breast
41	chr12:104136200-104136600	Enhancers	NH-A	brain
42	chr12:104136200-104136800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:104136200-104136800	Active TSS	Brain Substantia Nigra	brain

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