Variant report

Variant	rs2244554
Chromosome Location	chr8:98963242-98963243
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:98961024..98963389-chr8:99054505..99057436,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156482	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2444883	0.91[JPT][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2512028	0.91[JPT][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3018906	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription 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	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv1028055	chr8:98780445-98977746	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv891214	chr8:98849303-98990399	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv891215	chr8:98910287-98980663	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv528695	chr8:98960813-99022009	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2244554	NCALD	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:98938200-98969200	Weak transcription	Colonic Mucosa	Colon
2	chr8:98941000-98968000	Weak transcription	Esophagus	oesophagus
3	chr8:98945600-98970200	Weak transcription	Spleen	Spleen
4	chr8:98950400-98964600	Weak transcription	Pancreas	Pancrea
5	chr8:98956600-98968800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr8:98956600-98973600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr8:98957200-98970800	Weak transcription	Colon Smooth Muscle	Colon
8	chr8:98957200-98973600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr8:98957800-98969200	Weak transcription	Left Ventricle	heart
10	chr8:98961400-98964400	Enhancers	Ovary	ovary
11	chr8:98961800-98963800	Enhancers	Brain Angular Gyrus	brain
12	chr8:98961800-98963800	Enhancers	Brain Hippocampus Middle	brain
13	chr8:98961800-98964200	Enhancers	Brain Anterior Caudate	brain
14	chr8:98962000-98963600	Enhancers	NHDF-Ad	bronchial
15	chr8:98962000-98965000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr8:98962000-98965000	Enhancers	Brain Substantia Nigra	brain
17	chr8:98962000-98965600	Enhancers	Fetal Stomach	stomach
18	chr8:98962200-98965000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr8:98962200-98965000	Enhancers	Brain Cingulate Gyrus	brain
20	chr8:98962200-98965200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr8:98962200-98965200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr8:98962400-98963400	Enhancers	Stomach Smooth Muscle	stomach
23	chr8:98962400-98963600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr8:98962400-98963600	Enhancers	Osteobl	bone
25	chr8:98962400-98964200	Enhancers	NHLF	lung
26	chr8:98962600-98963800	Enhancers	Placenta Amnion	Placenta Amnion
27	chr8:98962600-98964000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr8:98962600-98965400	Enhancers	Fetal Muscle Leg	muscle
29	chr8:98962600-98965600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr8:98962800-98964800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr8:98962800-98965000	Enhancers	Fetal Lung	lung
32	chr8:98963000-98963400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr8:98963000-98963600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr8:98963000-98963600	Enhancers	Adipose Nuclei	Adipose
35	chr8:98963000-98963600	Enhancers	Fetal Heart	heart
36	chr8:98963000-98963800	Enhancers	Fetal Muscle Trunk	muscle
37	chr8:98963000-98964200	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr8:98963000-98964600	Enhancers	HSMM	muscle
39	chr8:98963000-98964800	Enhancers	HSMMtube	muscle
40	chr8:98963000-98965000	Enhancers	Muscle Satellite Cultured Cells	--
41	chr8:98963000-98965000	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr8:98963000-98965400	Enhancers	Right Atrium	heart
43	chr8:98963200-98963400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr8:98963200-98963400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr8:98963200-98963400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr8:98963200-98963400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr8:98963200-98963400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr8:98963200-98963400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
49	chr8:98963200-98963400	Enhancers	Fetal Brain Male	brain
50	chr8:98963200-98963600	Enhancers	Rectal Smooth Muscle	rectum

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