Variant report

Variant	rs10774543
Chromosome Location	chr12:120659997-120659998
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:120659632-120660522	U87	brain:	n/a	n/a
2	POLR2A	chr12:120656371-120661011	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr12:120659989-120660815	K562	blood:	n/a	n/a
4	POLR2A	chr12:120659915-120660437	U87	brain:	n/a	n/a
5	POLR2A	chr12:120659797-120660249	K562	blood:	n/a	n/a
6	POLR2A	chr12:120658123-120660469	Hela-S3	cervix:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120637654..120639331-chr12:120657599..120660175,2	K562	blood:
2	chr12:120642171..120684465-chr12:120719749..120734210,267	K562	blood:
3	chr12:120656223..120689871-chr12:120720394..120738112,311	MCF-7	breast:
4	chr12:120657004..120683911-chr12:120723753..120737731,232	K562	blood:

No data

Variant related genes	Relation type
PXN	TF binding region
ENSG00000089157	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000123009	Chromatin interaction
ENSG00000255857	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10735071	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12230540	0.89[EUR][1000 genomes]
rs12308065	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2286046	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2696029	1.00[JPT][hapmap]
rs3845191	1.00[ASN][1000 genomes]
rs3956837	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766959	0.92[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767884	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6490286	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6490287	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298516	1.00[JPT][hapmap]
rs7960843	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7968689	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7978656	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs965791	1.00[JPT][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	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	484 gene(s)	inside rSNPs	diseases
7	nsv1035698	chr12:120645330-120777580	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
8	nsv1047447	chr12:120645330-120808621	Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
9	esv3448120	chr12:120657469-120661667	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10774543	NME2P1	cis	parietal	SCAN
rs10774543	GCN1L1	cis	parietal	SCAN
rs10774543	DYNLL1	cis	parietal	SCAN
rs10774543	CCDC64	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120640200-120661800	Weak transcription	GM12878-XiMat	blood
2	chr12:120640200-120662400	Weak transcription	Fetal Brain Male	brain
3	chr12:120643800-120661800	Strong transcription	Fetal Muscle Leg	muscle
4	chr12:120644000-120660400	Strong transcription	Fetal Intestine Small	intestine
5	chr12:120644000-120662600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:120644800-120661400	Strong transcription	Fetal Intestine Large	intestine
7	chr12:120646400-120662400	Weak transcription	Right Atrium	heart
8	chr12:120647000-120661400	Strong transcription	Duodenum Mucosa	Duodenum
9	chr12:120647200-120661400	Strong transcription	Fetal Muscle Trunk	muscle
10	chr12:120647400-120661600	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr12:120647600-120660000	Strong transcription	Stomach Smooth Muscle	stomach
12	chr12:120647600-120661400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:120647600-120661400	Strong transcription	Pancreas	Pancrea
14	chr12:120647600-120661800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:120647600-120661800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:120647600-120661800	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr12:120647600-120662000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:120647600-120662000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:120647600-120662000	Strong transcription	Adipose Nuclei	Adipose
20	chr12:120647600-120662600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:120647600-120662600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr12:120647600-120662600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:120647600-120662600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:120647800-120660800	Strong transcription	HUVEC	blood vessel
25	chr12:120647800-120661600	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr12:120647800-120661600	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:120647800-120661800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr12:120647800-120662200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr12:120648000-120662200	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr12:120648000-120662800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:120648000-120662800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:120648200-120662200	Strong transcription	Fetal Stomach	stomach
33	chr12:120649600-120661800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:120649600-120661800	Weak transcription	Fetal Heart	heart
35	chr12:120649800-120661600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:120650000-120661400	Strong transcription	Colonic Mucosa	Colon
37	chr12:120650200-120661400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr12:120650600-120661400	Strong transcription	NHEK	skin
39	chr12:120651800-120661400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:120654000-120661400	Strong transcription	Placenta	Placenta
41	chr12:120654800-120660400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr12:120655200-120661800	Strong transcription	Primary T cells from cord blood	blood
43	chr12:120655200-120662600	Strong transcription	NHDF-Ad	bronchial
44	chr12:120655200-120665400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr12:120655600-120661400	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr12:120655800-120662400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr12:120656000-120661800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:120656200-120661400	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr12:120656200-120661600	Strong transcription	Osteobl	bone
50	chr12:120656200-120661800	Strong transcription	Duodenum Smooth Muscle	Duodenum

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