Variant report

Variant	rs11678403
Chromosome Location	chr2:48550497-48550498
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48550065..48552046-chr2:48557575..48559707,2	MCF-7	breast:
2	chr2:48549627..48551864-chr2:48552790..48555987,3	K562	blood:
3	chr2:48541080..48542668-chr2:48550192..48552132,2	MCF-7	breast:
4	chr2:48550181..48552303-chr2:48565867..48568039,2	K562	blood:

Variant related genes	Relation type
ENSG00000251889	Chromatin interaction
ENSG00000170802	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11682633	0.83[ASN][1000 genomes]
rs11684517	0.94[ASN][1000 genomes]
rs11688481	0.83[ASN][1000 genomes]
rs11690845	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17037289	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55761545	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57131168	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57537506	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59697023	0.83[ASN][1000 genomes]
rs72818477	0.83[EUR][1000 genomes]
rs72818491	0.82[ASN][1000 genomes]
rs72818494	0.82[ASN][1000 genomes]
rs72818502	0.82[ASN][1000 genomes]
rs72820403	0.83[ASN][1000 genomes]
rs72820404	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs72820409	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs72820416	0.83[AFR][1000 genomes]
rs72820418	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72820420	0.83[AFR][1000 genomes]
rs72820422	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs72820427	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7559431	0.89[EUR][1000 genomes]

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	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer 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	30 gene(s)	inside rSNPs	diseases
2	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv874002	chr2:48547751-48610367	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11678403	GTF2A1L	cis	Esophagus Muscularis	GTEx
rs11678403	PPP1R21	cis	Thyroid	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48543200-48553200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:48543400-48551800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:48543400-48552000	Weak transcription	Stomach Mucosa	stomach
4	chr2:48543400-48553000	Weak transcription	Lung	lung
5	chr2:48543400-48553000	Weak transcription	Psoas Muscle	Psoas
6	chr2:48543400-48568600	Weak transcription	HSMM	muscle
7	chr2:48543600-48551000	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr2:48543600-48552000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr2:48543600-48552200	Weak transcription	Osteobl	bone
10	chr2:48543600-48553200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:48543600-48553400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:48543600-48554400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:48543600-48555400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:48543600-48556600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr2:48543600-48559400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:48543600-48561000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:48543600-48570600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:48544200-48559600	Weak transcription	Fetal Kidney	kidney
19	chr2:48544400-48551200	Weak transcription	HUVEC	blood vessel
20	chr2:48544400-48552000	Weak transcription	Hela-S3	cervix
21	chr2:48544400-48556200	Weak transcription	NHDF-Ad	bronchial
22	chr2:48544400-48558600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:48544400-48570400	Weak transcription	NHEK	skin
24	chr2:48544400-48570800	Weak transcription	HMEC	breast
25	chr2:48544600-48558600	Weak transcription	Spleen	Spleen
26	chr2:48544600-48564400	Weak transcription	Fetal Intestine Small	intestine
27	chr2:48544800-48559400	Weak transcription	Right Atrium	heart
28	chr2:48545200-48551000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr2:48545800-48552000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:48546000-48550600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr2:48546000-48551800	Weak transcription	Brain Anterior Caudate	brain
32	chr2:48546000-48552000	Weak transcription	Brain Angular Gyrus	brain
33	chr2:48546400-48552000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:48546400-48552000	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr2:48546400-48552000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:48546600-48551400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:48546600-48556200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:48547000-48551400	Weak transcription	K562	blood
39	chr2:48547400-48554600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:48548000-48552000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:48548200-48550600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:48548200-48552000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:48548200-48552200	Weak transcription	Liver	Liver
44	chr2:48548200-48555200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:48548400-48551400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:48548400-48551600	Weak transcription	A549	lung
47	chr2:48548400-48551800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:48548400-48552400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:48548400-48553000	Weak transcription	Small Intestine	intestine
50	chr2:48548400-48553200	Weak transcription	Adipose Nuclei	Adipose

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