Variant report

Variant	rs4849088
Chromosome Location	chr2:113399493-113399494
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr2:113398297-113399601	K562	blood:	n/a	chr2:113399438-113399448
2	POLR2A	chr2:113397694-113399879	U87	brain:	n/a	n/a
3	MAX	chr2:113398390-113399608	NB4	blood:	n/a	chr2:113399438-113399448
4	RCOR1	chr2:113397515-113399670	IMR90	lung:	n/a	n/a
5	POLR2A	chr2:113397844-113399679	U87	brain:	n/a	n/a
6	JUN	chr2:113398110-113399563	K562	blood:	n/a	chr2:113398544-113398551 chr2:113398740-113398750 chr2:113398543-113398552
7	POLR2A	chr2:113397976-113399510	U87	brain:	n/a	n/a
8	POLR2A	chr2:113397872-113399688	IMR90	lung:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113379636..113386577-chr2:113398111..113406278,16	MCF-7	breast:
2	chr2:113398028..113400267-chr2:113464007..113465534,2	K562	blood:
3	chr2:113396800..113399610-chr2:113484528..113487337,2	MCF-7	breast:
4	chr2:113358188..113360377-chr2:113398948..113401833,2	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CKAP2L-1	chr2:113399484-113399559	XLOC_002275
2	lnc-CKAP2L-1	chr2:113399407-113399559	XLOC_002275
3	lnc-CKAP2L-1	chr2:113399409-113399559	ENSG00000237753
4	lnc-CKAP2L-1	chr2:113399419-113399559	NONHSAT073709

No data

Variant related genes	Relation type
SLC20A1	TF binding region
ENSG00000144130	Chromatin interaction
ENSG00000231747	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10177499	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10199279	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1061254	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10746527	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10779886	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11123144	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12994441	0.83[EUR][1000 genomes]
rs12996187	1.00[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs13023311	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17042199	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs2312699	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34109218	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs3936697	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4630766	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4848286	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4849087	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4849089	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4849090	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4849092	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4849093	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4849094	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4849095	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4849096	0.87[AMR][1000 genomes]
rs4849100	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56092429	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61443276	0.83[EUR][1000 genomes]
rs6542069	0.80[EUR][1000 genomes]
rs6737094	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6747638	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6747928	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6751117	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6793	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72948491	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7558138	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7559775	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs885346	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[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
rs4849088	AC079922.3	cis	Whole Blood	GTEx
rs4849088	AC079922.3	cis	Adipose Subcutaneous	GTEx
rs4849088	AC079922.3	cis	Artery Aorta	GTEx
rs4849088	AC079922.3	cis	Esophagus Mucosa	GTEx
rs4849088	AC079922.3	cis	Esophagus Muscularis	GTEx
rs4849088	AC079922.3	cis	Heart Left Ventricle	GTEx
rs4849088	AC079922.3	cis	Nerve Tibial	GTEx
rs4849088	AC079922.3	cis	Muscle Skeletal	GTEx
rs4849088	AC079922.3	cis	Thyroid	GTEx
rs4849088	AC079922.3	cis	Artery Tibial	GTEx
rs4849088	AC079922.3	cis	lung	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113385000-113402600	Weak transcription	Esophagus	oesophagus
2	chr2:113385800-113401800	Weak transcription	Brain Hippocampus Middle	brain
3	chr2:113389400-113402000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:113389600-113402200	Weak transcription	Primary B cells from cord blood	blood
5	chr2:113389800-113400400	Weak transcription	Fetal Intestine Small	intestine
6	chr2:113392800-113402000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:113394400-113402000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr2:113394600-113402000	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:113394800-113402000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:113395000-113400200	Weak transcription	Primary T cells from cord blood	blood
11	chr2:113395000-113401400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:113395000-113402000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr2:113395200-113401800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr2:113395600-113400800	Weak transcription	Liver	Liver
15	chr2:113396800-113400400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:113397000-113401800	Enhancers	HMEC	breast
17	chr2:113397200-113402000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:113397400-113401600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:113397600-113399600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:113397600-113402200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr2:113397800-113399600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr2:113397800-113399600	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr2:113397800-113399800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:113398000-113399600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr2:113398000-113399800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:113398000-113400400	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr2:113398000-113401600	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr2:113398000-113402000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:113398200-113399600	Enhancers	GM12878-XiMat	blood
30	chr2:113398200-113401400	Enhancers	HepG2	liver
31	chr2:113398200-113401800	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:113398400-113399600	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr2:113398400-113402400	Weak transcription	Aorta	Aorta
34	chr2:113398600-113401600	Weak transcription	Right Ventricle	heart
35	chr2:113398600-113401800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr2:113398600-113402200	Weak transcription	Left Ventricle	heart
37	chr2:113398600-113402200	Enhancers	NHDF-Ad	bronchial
38	chr2:113398800-113399600	Enhancers	Stomach Mucosa	stomach
39	chr2:113398800-113399800	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr2:113398800-113402000	Enhancers	HUVEC	blood vessel
41	chr2:113398800-113402200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:113398800-113402400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:113398800-113402400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:113398800-113402400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr2:113399000-113399600	Enhancers	NHEK	skin
46	chr2:113399000-113401200	Enhancers	K562	blood
47	chr2:113399000-113401800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:113399000-113401800	Enhancers	NH-A	brain
49	chr2:113399000-113402000	Weak transcription	Adipose Nuclei	Adipose
50	chr2:113399000-113402000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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