Variant report

Variant	rs2444878
Chromosome Location	chr8:98970147-98970148
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:98964671..98967862-chr8:98969521..98972694,3	MCF-7	breast:
2	chr8:98966806..98971038-chr8:98972037..98974632,4	K562	blood:
3	chr8:98969704..98971901-chr8:98988416..98991010,2	MCF-7	breast:
4	chr8:98968508..98970567-chr8:98972102..98974220,2	K562	blood:

Variant related genes	Relation type
ENSG00000132561	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1470957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2444880	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2444881	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2512030	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2512032	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2513844	0.82[JPT][hapmap]
rs3816496	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs897189	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

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
rs2444878	GRHL2	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:98945600-98970200	Weak transcription	Spleen	Spleen
2	chr8:98956600-98973600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr8:98957200-98970800	Weak transcription	Colon Smooth Muscle	Colon
4	chr8:98957200-98973600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr8:98963400-98976000	Weak transcription	Fetal Brain Male	brain
6	chr8:98963800-98970600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr8:98963800-98975200	Weak transcription	Placenta	Placenta
8	chr8:98964600-98970800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr8:98964800-98970800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr8:98964800-98976400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr8:98965000-98973600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr8:98965000-98980200	Weak transcription	Liver	Liver
13	chr8:98965600-98970400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr8:98965600-98983200	Weak transcription	NHLF	lung
15	chr8:98966600-98971000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr8:98968000-98976200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr8:98968200-98976200	Weak transcription	Gastric	stomach
18	chr8:98968200-98993800	Weak transcription	Esophagus	oesophagus
19	chr8:98968400-98973600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr8:98968400-98973600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr8:98968600-98971400	Enhancers	Fetal Stomach	stomach
22	chr8:98968800-98970200	Enhancers	Brain Substantia Nigra	brain
23	chr8:98968800-98970600	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr8:98968800-98970600	Enhancers	Fetal Muscle Trunk	muscle
25	chr8:98968800-98971200	Enhancers	Ovary	ovary
26	chr8:98968800-98971600	Enhancers	Fetal Muscle Leg	muscle
27	chr8:98969000-98970200	Enhancers	Rectal Smooth Muscle	rectum
28	chr8:98969000-98971600	Enhancers	Adipose Nuclei	Adipose
29	chr8:98969200-98971000	Enhancers	Stomach Smooth Muscle	stomach
30	chr8:98969200-98971200	Enhancers	Left Ventricle	heart
31	chr8:98969200-98971200	Weak transcription	Stomach Mucosa	stomach
32	chr8:98969200-98971400	Enhancers	Right Atrium	heart
33	chr8:98969200-98979800	Weak transcription	Fetal Intestine Small	intestine
34	chr8:98969800-98970200	Weak transcription	Lung	lung
35	chr8:98969800-98970800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr8:98969800-98971000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr8:98969800-98971200	Weak transcription	Fetal Lung	lung
38	chr8:98969800-98982600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr8:98970000-98970200	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr8:98970000-98970800	Enhancers	Colonic Mucosa	Colon
41	chr8:98970000-98971000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr8:98970000-98971000	Weak transcription	Right Ventricle	heart
43	chr8:98970000-98984800	Weak transcription	Fetal Kidney	kidney
44	chr8:98970000-98985200	Weak transcription	Brain Angular Gyrus	brain
45	chr8:98970000-98992200	Weak transcription	Brain Hippocampus Middle	brain

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