Variant report

Variant	rs4849096
Chromosome Location	chr2:113423684-113423685
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113421512..113426143-chr2:113441172..113445759,7	K562	blood:
2	chr2:113423200..113424917-chr2:113426648..113428769,2	MCF-7	breast:
3	chr14:103058550..103061482-chr2:113422635..113424656,2	MCF-7	breast:
4	chr2:113422885..113426187-chr2:113430296..113432914,4	K562	blood:
5	chr2:113422747..113425498-chr2:113447887..113450877,2	K562	blood:
6	chr2:113422855..113425546-chr2:113428283..113429870,2	K562	blood:
7	chr2:113419485..113422218-chr2:113423311..113426993,3	K562	blood:

Variant related genes	Relation type
ENSG00000089902	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10199279	0.87[AMR][1000 genomes]
rs1061254	0.87[AMR][1000 genomes]
rs10746527	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10779886	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11123144	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11123145	0.90[AFR][1000 genomes]
rs13023311	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1516791	0.82[AFR][1000 genomes]
rs2312699	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs3936697	0.84[AMR][1000 genomes]
rs4630766	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4848286	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4849088	0.87[AMR][1000 genomes]
rs4849089	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4849090	0.87[AMR][1000 genomes]
rs4849092	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4849093	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4849094	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4849095	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4849100	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56092429	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61443276	0.92[EUR][1000 genomes]
rs6737094	0.87[AMR][1000 genomes]
rs6747638	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6747928	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6751117	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6793	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72948491	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7558138	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs885346	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[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	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer 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 target site	51 gene(s)	inside rSNPs	diseases
4	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4849096	AC079922.3	cis	Artery Tibial	GTEx
rs4849096	AC079922.3	cis	Heart Left Ventricle	GTEx
rs4849096	AC079922.3	cis	Thyroid	GTEx
rs4849096	AC079922.3	cis	Adipose Subcutaneous	GTEx
rs4849096	AC079922.3	cis	Whole Blood	GTEx
rs4849096	AC079922.3	cis	Muscle Skeletal	GTEx
rs4849096	AC079922.3	cis	lung	GTEx
rs4849096	AC079922.3	cis	Esophagus Mucosa	GTEx
rs4849096	AC079922.3	cis	Nerve Tibial	GTEx
rs4849096	AC079922.3	cis	Esophagus Muscularis	GTEx
rs4849096	AC079922.3	cis	Artery Aorta	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113405200-113423800	Strong transcription	Fetal Muscle Trunk	muscle
2	chr2:113406200-113424600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:113411200-113428200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:113417200-113425400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:113417400-113426800	Weak transcription	Fetal Heart	heart
6	chr2:113417600-113424200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:113417600-113426000	Weak transcription	Esophagus	oesophagus
8	chr2:113418200-113423800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:113418200-113424600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr2:113418400-113424600	Strong transcription	Primary T cells from cord blood	blood
11	chr2:113418800-113424600	Weak transcription	Fetal Kidney	kidney
12	chr2:113418800-113428600	Weak transcription	Brain Substantia Nigra	brain
13	chr2:113419200-113424200	Weak transcription	Stomach Mucosa	stomach
14	chr2:113419600-113423800	Weak transcription	Fetal Lung	lung
15	chr2:113419600-113424000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:113419600-113424400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:113419600-113431200	Weak transcription	Aorta	Aorta
18	chr2:113420400-113424800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:113420600-113423800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:113420800-113424400	Weak transcription	Brain Angular Gyrus	brain
21	chr2:113420800-113424800	Strong transcription	A549	lung
22	chr2:113420800-113426000	Weak transcription	Gastric	stomach
23	chr2:113420800-113431200	Weak transcription	Primary B cells from cord blood	blood
24	chr2:113421000-113424000	Weak transcription	Ovary	ovary
25	chr2:113421000-113424000	Weak transcription	Hela-S3	cervix
26	chr2:113421000-113424200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr2:113421000-113426200	Weak transcription	Brain Anterior Caudate	brain
28	chr2:113421200-113425600	Weak transcription	Right Ventricle	heart
29	chr2:113421200-113431400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:113421400-113424600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr2:113421400-113448400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:113421600-113423800	Weak transcription	HepG2	liver
33	chr2:113421600-113427200	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:113421600-113429400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:113421600-113429400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr2:113421600-113438400	Weak transcription	Psoas Muscle	Psoas
37	chr2:113421800-113424800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:113422000-113426000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr2:113422200-113432000	Weak transcription	Left Ventricle	heart
40	chr2:113422400-113424200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:113422400-113426200	Weak transcription	Colonic Mucosa	Colon
42	chr2:113422400-113427000	Weak transcription	Brain Hippocampus Middle	brain
43	chr2:113422600-113424400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:113422600-113429400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:113422600-113431600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr2:113422600-113432000	Weak transcription	Fetal Muscle Leg	muscle
47	chr2:113422800-113428000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:113422800-113431400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:113422800-113437000	Weak transcription	HMEC	breast
50	chr2:113422800-113438200	Weak transcription	Brain Cingulate Gyrus	brain

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