Variant report

Variant	rs1868246
Chromosome Location	chr4:87849082-87849083
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87848034..87854001-chr4:87854592..87858265,8	MCF-7	breast:
2	chr4:87846751..87849645-chr4:87881394..87883091,2	K562	blood:
3	chr4:87845889..87863516-chr4:87925389..87935181,79	K562	blood:
4	chr4:87847594..87849419-chr4:87893253..87895027,2	MCF-7	breast:
5	chr4:87846783..87849156-chr4:87926665..87928343,2	K562	blood:
6	chr4:87845043..87846652-chr4:87847978..87849519,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12506662	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1447993	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17012186	0.92[CHB][hapmap]
rs1992876	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[MEX][hapmap]
rs2442078	0.93[EUR][1000 genomes]
rs2705621	0.94[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2869632	0.92[CHB][hapmap]
rs2904151	0.92[CHB][hapmap];0.89[CHD][hapmap];0.92[MEX][hapmap]
rs3775229	0.82[CHD][hapmap]
rs3775230	0.86[CHD][hapmap]
rs6419117	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6836128	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs725030	0.92[CHB][hapmap];0.89[CHD][hapmap];0.82[MEX][hapmap]
rs72613147	0.89[ASN][1000 genomes]
rs72613148	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72613149	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671931	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9996533	0.81[AMR][1000 genomes];0.92[EUR][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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1868246	KLHL8	cis	cerebellum	SCAN
rs1868246	HERC6	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87825600-87849400	Weak transcription	Lung	lung
2	chr4:87825600-87849400	Weak transcription	Spleen	Spleen
3	chr4:87825800-87854800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr4:87825800-87854800	Weak transcription	Right Ventricle	heart
5	chr4:87825800-87855200	Weak transcription	Fetal Stomach	stomach
6	chr4:87826000-87852400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr4:87829800-87855000	Weak transcription	Aorta	Aorta
8	chr4:87830200-87849600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:87830200-87855200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr4:87830400-87849400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:87830400-87854600	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:87831000-87855000	Weak transcription	Fetal Lung	lung
13	chr4:87831400-87854400	Weak transcription	Fetal Heart	heart
14	chr4:87831400-87854800	Weak transcription	Right Atrium	heart
15	chr4:87832200-87854800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr4:87837200-87854400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:87838400-87855000	Weak transcription	Colonic Mucosa	Colon
18	chr4:87839000-87850200	Enhancers	Placenta	Placenta
19	chr4:87840200-87852200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:87840200-87854800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:87842600-87855400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:87843600-87849200	Weak transcription	Adipose Nuclei	Adipose
23	chr4:87843800-87849200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr4:87843800-87854600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:87844000-87849200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr4:87844000-87849400	Weak transcription	Liver	Liver
27	chr4:87844000-87849400	Weak transcription	Esophagus	oesophagus
28	chr4:87844000-87854600	Weak transcription	Colon Smooth Muscle	Colon
29	chr4:87844000-87854800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:87844000-87854800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr4:87844000-87854800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr4:87844000-87855000	Weak transcription	Brain Substantia Nigra	brain
33	chr4:87844000-87855000	Weak transcription	Fetal Muscle Leg	muscle
34	chr4:87844200-87849200	Weak transcription	Ovary	ovary
35	chr4:87844400-87852200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:87845200-87849800	Enhancers	HUVEC	blood vessel
37	chr4:87845400-87849800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:87845400-87849800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:87845400-87850400	Enhancers	HMEC	breast
40	chr4:87845600-87849800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:87845600-87850000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:87845600-87854800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:87845800-87849800	Enhancers	NHLF	lung
44	chr4:87845800-87855200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:87846000-87850000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr4:87846400-87849200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr4:87846400-87852400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:87846400-87855400	Weak transcription	Gastric	stomach
49	chr4:87846600-87851400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr4:87846600-87854800	Weak transcription	Brain Anterior Caudate	brain

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