Variant report

Variant	rs848279
Chromosome Location	chr2:58419649-58419650
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:58418370..58420145-chr2:58421628..58423129,2	K562	blood:
2	chr2:58417379..58419777-chr2:58466970..58469419,2	K562	blood:

Variant related genes	Relation type
ENSG00000115392	Chromatin interaction
ENSG00000273063	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1016771	0.87[CEU][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap]
rs1051061	0.87[CEU][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap]
rs1100188	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1100191	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11678320	0.87[CEU][hapmap]
rs12999901	0.87[CEU][hapmap]
rs13011711	0.87[CEU][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap]
rs2110664	0.82[LWK][hapmap]
rs2691672	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35248619	0.81[AMR][1000 genomes]
rs3771213	0.86[CEU][hapmap]
rs3771216	0.86[LWK][hapmap]
rs6709460	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6727746	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs848278	0.91[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs848280	0.95[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs848281	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs848282	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs848284	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs848291	0.87[CEU][hapmap];0.80[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs848292	1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]

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	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1007527	chr2:58386271-58477536	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv535735	chr2:58386271-58477536	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv458052	chr2:58388696-58450569	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv582098	chr2:58388696-58450569	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv817995	chr2:58390538-58450569	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv1804150	chr2:58418501-58431168	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58349000-58421200	Weak transcription	Brain Substantia Nigra	brain
2	chr2:58359000-58454000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:58365600-58438000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:58385000-58421200	Weak transcription	Left Ventricle	heart
5	chr2:58385200-58424600	Weak transcription	Ovary	ovary
6	chr2:58388800-58437400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:58389000-58423200	Weak transcription	NHLF	lung
8	chr2:58389600-58431000	Weak transcription	HUVEC	blood vessel
9	chr2:58389800-58421000	Weak transcription	K562	blood
10	chr2:58390200-58421200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:58391000-58467000	Weak transcription	HMEC	breast
12	chr2:58396400-58438000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:58396400-58438000	Weak transcription	Pancreas	Pancrea
14	chr2:58397800-58442600	Weak transcription	Brain Anterior Caudate	brain
15	chr2:58398000-58437800	Weak transcription	Primary B cells from cord blood	blood
16	chr2:58399400-58437400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:58399800-58421800	Weak transcription	Fetal Stomach	stomach
18	chr2:58399800-58426000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:58400400-58437800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:58403000-58439400	Weak transcription	HSMM	muscle
21	chr2:58403600-58434000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:58403600-58437200	Weak transcription	Fetal Brain Female	brain
23	chr2:58407400-58424000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:58407600-58425000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:58410400-58425200	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:58411600-58437400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:58412000-58420800	Weak transcription	GM12878-XiMat	blood
28	chr2:58413400-58420000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:58413800-58425000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr2:58413800-58438000	Weak transcription	Thymus	Thymus
31	chr2:58414000-58437600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:58414000-58461400	Weak transcription	NHEK	skin
33	chr2:58414200-58429800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:58414200-58435800	Weak transcription	Fetal Intestine Small	intestine
35	chr2:58414400-58438000	Weak transcription	Esophagus	oesophagus
36	chr2:58414600-58425000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:58414600-58437400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:58414600-58437400	Weak transcription	Brain Germinal Matrix	brain
39	chr2:58415000-58430400	Weak transcription	NHDF-Ad	bronchial
40	chr2:58415000-58437600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:58415200-58422400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr2:58415400-58421000	Weak transcription	Hela-S3	cervix
43	chr2:58415400-58434000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr2:58415800-58437400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:58416000-58437400	Weak transcription	Fetal Kidney	kidney
46	chr2:58416200-58420800	Weak transcription	A549	lung
47	chr2:58416200-58421000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr2:58416200-58437400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:58416200-58454200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:58416400-58420600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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