Variant report

Variant	rs2444907
Chromosome Location	chr8:98934748-98934749
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	chr8:98933138..98936017-chr8:98937438..98939186,2	MCF-7	breast:
2	chr8:98933283..98934888-chr8:98936551..98939414,2	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12676720	0.88[CEU][hapmap];0.83[CHB][hapmap];0.86[MEX][hapmap]
rs13248439	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs13256241	0.88[CEU][hapmap];0.83[CHB][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs2290470	0.84[CEU][hapmap];0.81[CHB][hapmap];0.86[MEX][hapmap]
rs2444905	0.86[ASN][1000 genomes]
rs2512069	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2513822	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2513834	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs753799	0.96[CEU][hapmap];0.83[CHB][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2444907	PGCP	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:98929200-98944800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr8:98929400-98934800	Weak transcription	Adipose Nuclei	Adipose
3	chr8:98929600-98935000	Weak transcription	Fetal Kidney	kidney
4	chr8:98929600-98938000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr8:98929800-98936600	Weak transcription	Fetal Lung	lung
6	chr8:98929800-98937800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr8:98930800-98950000	Weak transcription	Right Ventricle	heart
8	chr8:98931000-98938600	Weak transcription	Placenta	Placenta
9	chr8:98931000-98940800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr8:98931200-98934800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr8:98931200-98934800	Weak transcription	Osteobl	bone
12	chr8:98931200-98935000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr8:98931200-98935000	Weak transcription	NHDF-Ad	bronchial
14	chr8:98931200-98938000	Weak transcription	NH-A	brain
15	chr8:98931200-98938400	Weak transcription	Left Ventricle	heart
16	chr8:98931200-98944200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr8:98931400-98935000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr8:98931600-98937800	Weak transcription	Fetal Intestine Large	intestine
19	chr8:98931600-98938200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr8:98931800-98943200	Enhancers	Fetal Muscle Leg	muscle
21	chr8:98932000-98940800	Weak transcription	Ovary	ovary
22	chr8:98932200-98943400	Weak transcription	Pancreas	Pancrea
23	chr8:98932400-98934800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr8:98932400-98936400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr8:98932400-98940600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr8:98932800-98935400	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr8:98933000-98935400	Enhancers	Brain Anterior Caudate	brain
28	chr8:98933000-98935400	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr8:98933000-98935800	Enhancers	Brain Cingulate Gyrus	brain
30	chr8:98933000-98936800	Enhancers	Brain Hippocampus Middle	brain
31	chr8:98933200-98934800	Enhancers	Brain Substantia Nigra	brain
32	chr8:98933200-98935200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr8:98933200-98935200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr8:98933200-98935400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr8:98933200-98935800	Enhancers	Brain Angular Gyrus	brain
36	chr8:98933200-98936400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr8:98933600-98934800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr8:98933800-98934800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr8:98933800-98935200	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr8:98933800-98935400	Enhancers	H1 Cell Line	embryonic stem cell
41	chr8:98934000-98935400	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr8:98934000-98935400	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr8:98934000-98935800	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr8:98934000-98937600	Weak transcription	Fetal Stomach	stomach
45	chr8:98934200-98935200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr8:98934200-98943400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr8:98934400-98935000	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr8:98934600-98934800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr8:98934600-98935200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr8:98934600-98936000	Enhancers	Right Atrium	heart

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