Variant report

Variant	rs2240108
Chromosome Location	chr12:48180508-48180509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:48180407-48181090	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:48178680-48181059	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr12:48168539-48189348	K562	blood:	n/a	n/a
4	POLR2A	chr12:48174566-48182409	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr12:48180152-48180734	A549	lung:	n/a	n/a
6	POLR2A	chr12:48178708-48181303	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr12:48178554-48181002	A549	lung:	n/a	n/a
8	POLR2A	chr12:48174592-48181015	K562	blood:	n/a	n/a
9	POLR2A	chr12:48174465-48181100	K562	blood:	n/a	n/a
10	POLR2A	chr12:48179951-48181150	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:48177447..48181370-chr12:48191436..48194487,4	K562	blood:
2	chr12:48178543..48181297-chr12:48188884..48191254,2	MCF-7	breast:
3	chr12:48180097..48182896-chr12:48212671..48214919,5	MCF-7	breast:
4	chr12:48178200..48181079-chr12:48195107..48197877,2	K562	blood:
5	chr12:48141986..48143850-chr12:48180464..48183428,2	MCF-7	breast:
6	chr12:48178905..48182069-chr12:48186419..48189254,4	K562	blood:
7	chr12:48179712..48182344-chr12:48183678..48185833,2	MCF-7	breast:
8	chr12:48178059..48181422-chr12:48185905..48188715,3	K562	blood:

No data

Variant related genes	Relation type
HDAC7	TF binding region
ENSG00000079337	Chromatin interaction
ENSG00000061273	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11608804	0.97[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2072116	1.00[CHD][hapmap]
rs3759408	0.86[AMR][1000 genomes]
rs7138076	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73105899	0.92[AMR][1000 genomes]
rs73107911	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs757282	1.00[CHD][hapmap]
rs886431	1.00[CHD][hapmap]

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	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer 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	75 gene(s)	inside rSNPs	diseases
3	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
4	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
5	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
9	nsv899060	chr12:48180508-48231430	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2240108	HDAC7	cis	cerebellum	SCAN
rs2240108	C16orf61	trans	parietal	SCAN
rs2240108	ADAMTS20	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48168200-48195200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:48169800-48181200	Weak transcription	GM12878-XiMat	blood
3	chr12:48170600-48181200	Weak transcription	HepG2	liver
4	chr12:48173000-48192400	Weak transcription	Right Atrium	heart
5	chr12:48173200-48191200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr12:48173600-48187600	Weak transcription	Fetal Heart	heart
7	chr12:48173800-48193800	Strong transcription	Gastric	stomach
8	chr12:48173800-48195400	Strong transcription	Fetal Stomach	stomach
9	chr12:48174000-48193000	Strong transcription	Placenta	Placenta
10	chr12:48174600-48191600	Strong transcription	Thymus	Thymus
11	chr12:48174600-48192200	Strong transcription	Lung	lung
12	chr12:48174600-48192600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:48174600-48193200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:48174600-48193400	Strong transcription	Brain Germinal Matrix	brain
15	chr12:48174600-48195600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:48174800-48181800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:48174800-48184800	Strong transcription	Spleen	Spleen
18	chr12:48174800-48191400	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:48174800-48192000	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:48174800-48192000	Strong transcription	Ovary	ovary
21	chr12:48174800-48192400	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr12:48174800-48192800	Strong transcription	Primary T cells from cord blood	blood
23	chr12:48174800-48194600	Strong transcription	Fetal Intestine Large	intestine
24	chr12:48175000-48180600	Strong transcription	Duodenum Mucosa	Duodenum
25	chr12:48175000-48191800	Strong transcription	Colonic Mucosa	Colon
26	chr12:48175000-48193000	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr12:48175000-48193000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:48175000-48193200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr12:48175000-48193200	Strong transcription	NHLF	lung
30	chr12:48175000-48193200	Strong transcription	Osteobl	bone
31	chr12:48175000-48193400	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr12:48175200-48191400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:48175200-48193600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:48175400-48190800	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr12:48175400-48191000	Strong transcription	Primary hematopoietic stem cells	blood
36	chr12:48175400-48191400	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr12:48175400-48191400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr12:48175400-48192800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:48175600-48185200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:48175600-48185400	Strong transcription	Liver	Liver
41	chr12:48175600-48185800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:48175600-48190800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:48175600-48191000	Strong transcription	Hela-S3	cervix
44	chr12:48175600-48191400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr12:48175600-48191400	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr12:48175600-48192400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:48175600-48192800	Strong transcription	Aorta	Aorta
48	chr12:48175600-48195000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:48175600-48195800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:48175800-48185400	Strong transcription	Primary B cells from cord blood	blood

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