Variant report

Variant	rs10744748
Chromosome Location	chr12:120561836-120561837
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:120559913..120564774-chr12:120629381..120633870,5	MCF-7	breast:
2	chr12:120561828..120564704-chr12:120575956..120578442,3	K562	blood:
3	chr12:120560646..120564537-chr12:120726297..120728813,4	MCF-7	breast:
4	chr12:120561767..120563673-chr12:120616678..120618274,2	K562	blood:
5	chr12:120561796..120564590-chr12:120575330..120577438,3	K562	blood:
6	chr12:120561375..120563129-chr12:120636617..120639172,3	K562	blood:
7	chr12:120560915..120562885-chr12:120637207..120639199,3	K562	blood:
8	chr12:120560112..120563743-chr12:120637060..120640117,5	MCF-7	breast:
9	chr12:120559989..120562800-chr12:120564491..120566220,2	MCF-7	breast:
10	chr12:120561187..120563003-chr12:120608631..120611553,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000089154	Chromatin interaction
ENSG00000263913	Chromatin interaction
ENSG00000089157	Chromatin interaction
ENSG00000255857	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10744749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065028	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11065035	0.82[JPT][hapmap]
rs11065036	0.82[JPT][hapmap]
rs1151824	0.81[CHB][hapmap]
rs1151825	0.81[CHB][hapmap]
rs1151827	0.81[CHB][hapmap]
rs12310433	0.82[JPT][hapmap]
rs12312562	0.82[JPT][hapmap]
rs1634814	0.81[CHB][hapmap]
rs2074540	0.82[JPT][hapmap]
rs2240312	0.86[JPT][hapmap]
rs2240317	0.82[JPT][hapmap]
rs2240318	0.82[JPT][hapmap]
rs2240321	0.82[JPT][hapmap]
rs2240322	0.82[JPT][hapmap]
rs2240323	0.82[JPT][hapmap]
rs2240325	0.87[JPT][hapmap]
rs2269941	0.82[JPT][hapmap]
rs2269944	0.82[JPT][hapmap]
rs2269945	0.82[JPT][hapmap]
rs2286049	0.82[JPT][hapmap]
rs2286050	0.82[JPT][hapmap]
rs2286051	0.82[JPT][hapmap]
rs2422	0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3742039	0.81[JPT][hapmap]
rs7134706	0.82[JPT][hapmap]
rs7296380	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10744748	GCN1L1	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120555800-120562200	Enhancers	Primary B cells from peripheral blood	blood
2	chr12:120555800-120563800	Weak transcription	Aorta	Aorta
3	chr12:120556000-120562200	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr12:120556200-120562400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:120556200-120562400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:120556400-120563800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:120556600-120563000	Weak transcription	Fetal Muscle Leg	muscle
8	chr12:120556600-120563000	Weak transcription	Gastric	stomach
9	chr12:120556600-120563600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:120556600-120563600	Weak transcription	Brain Anterior Caudate	brain
11	chr12:120556600-120563600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:120556600-120564000	Weak transcription	Lung	lung
13	chr12:120556800-120562400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr12:120556800-120563000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:120556800-120563200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:120556800-120563200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:120556800-120563400	Weak transcription	Right Ventricle	heart
18	chr12:120556800-120563600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:120556800-120563600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:120556800-120563600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:120556800-120563600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:120556800-120563600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:120556800-120563600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:120556800-120563800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:120556800-120563800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr12:120556800-120563800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr12:120556800-120563800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:120556800-120563800	Weak transcription	Brain Hippocampus Middle	brain
29	chr12:120556800-120563800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr12:120556800-120563800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr12:120556800-120564000	Weak transcription	Brain Angular Gyrus	brain
32	chr12:120556800-120564600	Weak transcription	Ovary	ovary
33	chr12:120556800-120564600	Weak transcription	K562	blood
34	chr12:120556800-120565000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:120556800-120565200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:120556800-120567000	Weak transcription	Fetal Lung	lung
37	chr12:120556800-120571800	Weak transcription	Fetal Brain Male	brain
38	chr12:120556800-120578200	Weak transcription	Fetal Heart	heart
39	chr12:120557000-120563200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:120557000-120563400	Weak transcription	Fetal Intestine Large	intestine
41	chr12:120557000-120563600	Weak transcription	Pancreas	Pancrea
42	chr12:120557000-120563800	Weak transcription	Dnd41	blood
43	chr12:120557000-120564000	Weak transcription	Left Ventricle	heart
44	chr12:120557000-120564400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:120557000-120565200	Weak transcription	Psoas Muscle	Psoas
46	chr12:120557200-120563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:120557200-120563400	Weak transcription	Fetal Intestine Small	intestine
48	chr12:120557400-120563200	Weak transcription	Brain Germinal Matrix	brain
49	chr12:120557600-120564000	Weak transcription	Brain Substantia Nigra	brain
50	chr12:120557600-120565200	Weak transcription	Small Intestine	intestine

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