Variant report

Variant	rs11675441
Chromosome Location	chr2:46601496-46601497
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:46599928-46602007	K562	blood:	n/a	n/a
2	POLR2A	chr2:46601011-46601918	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:46601066..46602772-chr2:46608160..46609687,2	MCF-7	breast:
2	chr2:46599672..46601854-chr2:46635973..46638690,2	K562	blood:
3	chr2:46600582..46603606-chr2:46603926..46607048,4	K562	blood:

Variant related genes	Relation type
EPAS1	TF binding region
ENSG00000116016	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10178633	0.85[CEU][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11675232	0.96[CEU][hapmap];0.84[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11675328	0.85[AMR][1000 genomes]
rs11678465	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11678817	0.88[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11681242	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11686705	0.86[AMR][1000 genomes]
rs11690951	0.89[CEU][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11691694	0.85[AMR][1000 genomes]
rs11692911	0.96[CEU][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11693596	0.84[AMR][1000 genomes]
rs11693754	0.86[AMR][1000 genomes]
rs11694193	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12467821	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006131	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1530622	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1530631	0.82[CEU][hapmap]
rs1868092	0.81[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1868093	0.81[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1868094	0.82[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3768730	0.88[CEU][hapmap]
rs4953356	0.82[CEU][hapmap]
rs4953358	0.82[CEU][hapmap]
rs4953359	0.85[CEU][hapmap]
rs55826825	0.85[AMR][1000 genomes]
rs56161503	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59034065	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62138871	0.84[AMR][1000 genomes]
rs6707241	0.80[CEU][hapmap]
rs6735812	0.82[CEU][hapmap]
rs6740096	0.81[CEU][hapmap]
rs6743991	0.81[CEU][hapmap]
rs6756667	0.81[CEU][hapmap]
rs7557402	0.92[CEU][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7567582	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7568285	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7583088	0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7583392	0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7591548	0.85[AMR][1000 genomes]
rs7594278	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7594912	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7598371	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7606559	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv916169	chr2:46310963-46622603	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46573200-46613000	Strong transcription	Hela-S3	cervix
2	chr2:46574600-46607200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:46574800-46613000	Weak transcription	HSMM	muscle
4	chr2:46586600-46604000	Weak transcription	HSMMtube	muscle
5	chr2:46588600-46604800	Weak transcription	Stomach Mucosa	stomach
6	chr2:46589800-46616600	Weak transcription	Thymus	Thymus
7	chr2:46591200-46606400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:46592000-46605000	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr2:46592200-46619800	Weak transcription	K562	blood
10	chr2:46592600-46606600	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr2:46592600-46608400	Strong transcription	Osteobl	bone
12	chr2:46592600-46611200	Weak transcription	Primary T cells from cord blood	blood
13	chr2:46592600-46612600	Strong transcription	NHEK	skin
14	chr2:46592600-46616200	Strong transcription	Placenta Amnion	Placenta Amnion
15	chr2:46593000-46602600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:46593000-46604000	Strong transcription	Adipose Nuclei	Adipose
17	chr2:46593600-46601600	Strong transcription	A549	lung
18	chr2:46593600-46615400	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:46594000-46612800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:46594200-46604400	Strong transcription	NHLF	lung
21	chr2:46594400-46615600	Strong transcription	Duodenum Mucosa	Duodenum
22	chr2:46594600-46601600	Strong transcription	Aorta	Aorta
23	chr2:46594600-46612800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:46594800-46604000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:46594800-46604000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:46594800-46604000	Strong transcription	Right Ventricle	heart
27	chr2:46594800-46615400	Strong transcription	Liver	Liver
28	chr2:46594800-46615600	Strong transcription	HUVEC	blood vessel
29	chr2:46595000-46604000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr2:46595000-46616000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:46595200-46602000	Weak transcription	Small Intestine	intestine
32	chr2:46595400-46602800	Strong transcription	Left Ventricle	heart
33	chr2:46595400-46603800	Weak transcription	Brain Angular Gyrus	brain
34	chr2:46595400-46603800	Weak transcription	Brain Hippocampus Middle	brain
35	chr2:46595800-46604000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:46595800-46604000	Weak transcription	Brain Substantia Nigra	brain
37	chr2:46596000-46605800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:46596000-46612800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr2:46596200-46605200	Strong transcription	Ovary	ovary
40	chr2:46596600-46604000	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr2:46596800-46602200	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:46596800-46603800	Weak transcription	Fetal Muscle Leg	muscle
43	chr2:46597600-46602600	Strong transcription	Lung	lung
44	chr2:46597800-46605800	Weak transcription	Fetal Heart	heart
45	chr2:46598000-46603800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr2:46598200-46605600	Weak transcription	Colon Smooth Muscle	Colon
47	chr2:46598400-46604000	Weak transcription	Fetal Intestine Large	intestine
48	chr2:46598400-46604200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:46598600-46604400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr2:46598800-46604800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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