Variant report

Variant	rs2738749
Chromosome Location	chr1:221059565-221059566
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:221049482..221052010-chr1:221057978..221059947,2	K562	blood:
2	chr1:221059069..221061749-chr1:221063321..221065597,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136630	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2491259	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2738750	0.83[AFR][1000 genomes]
rs2738754	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2784251	0.81[AFR][1000 genomes]
rs2784271	0.94[YRI][hapmap]
rs2784272	0.94[YRI][hapmap]
rs2807857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2807860	0.81[AFR][1000 genomes]
rs868058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv1798350	chr1:221020278-221069740	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2738749	RP11-295M18.2	cis	lung	GTEx
rs2738749	RP11-295M18.2	cis	Artery Tibial	GTEx
rs2738749	RP11-295M18.2	cis	Nerve Tibial	GTEx
rs2738749	RP11-295M18.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221054800-221061000	Weak transcription	HSMM	muscle
2	chr1:221055800-221060400	Weak transcription	Hela-S3	cervix
3	chr1:221056000-221061000	Weak transcription	NHDF-Ad	bronchial
4	chr1:221056200-221060400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:221056400-221060200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:221056600-221060000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:221056600-221060400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:221056800-221060400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:221057000-221060000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:221057000-221060200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:221057000-221060400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
12	chr1:221057000-221061800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr1:221057200-221059800	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:221057200-221060000	Strong transcription	NHLF	lung
15	chr1:221057400-221059600	Genic enhancers	Monocytes-CD14+_RO01746	blood
16	chr1:221057600-221060200	Strong transcription	Adipose Nuclei	Adipose
17	chr1:221057800-221060000	Strong transcription	Liver	Liver
18	chr1:221057800-221060200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
19	chr1:221058200-221060000	Strong transcription	Right Ventricle	heart
20	chr1:221058200-221060000	Strong transcription	Spleen	Spleen
21	chr1:221058200-221060200	Strong transcription	Left Ventricle	heart
22	chr1:221058200-221061200	Weak transcription	Psoas Muscle	Psoas
23	chr1:221058400-221059600	Genic enhancers	Duodenum Smooth Muscle	Duodenum
24	chr1:221058400-221059800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr1:221058400-221061000	Weak transcription	Aorta	Aorta
26	chr1:221058800-221060000	Strong transcription	Fetal Muscle Leg	muscle
27	chr1:221058800-221060000	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:221058800-221060800	Weak transcription	Pancreas	Pancrea
29	chr1:221058800-221061000	Weak transcription	Gastric	stomach
30	chr1:221059000-221059600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr1:221059000-221059800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:221059000-221060000	Strong transcription	Placenta	Placenta
33	chr1:221059000-221060000	Weak transcription	Lung	lung
34	chr1:221059000-221060200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:221059000-221060800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:221059000-221061000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr1:221059200-221059600	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr1:221059200-221060200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr1:221059200-221060600	Weak transcription	Osteobl	bone
40	chr1:221059200-221061000	Weak transcription	HSMMtube	muscle
41	chr1:221059400-221060400	Weak transcription	Primary B cells from cord blood	blood

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