Variant report

Variant	rs4871827
Chromosome Location	chr8:121061879-121061880
allele	A/G
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	RAD21	chr8:121061837-121062037	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000254343	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10095303	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10108373	1.00[YRI][hapmap]
rs10109558	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10110144	0.84[CHD][hapmap];0.82[MEX][hapmap]
rs1051534	0.83[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10738134	1.00[YRI][hapmap]
rs10955946	0.80[AMR][1000 genomes]
rs10955947	0.80[AMR][1000 genomes]
rs10955951	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11787175	0.86[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11787250	0.86[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11986202	0.80[AMR][1000 genomes]
rs11995866	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12546625	0.86[CHD][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap]
rs12680859	0.84[CHD][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap]
rs13266382	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13272368	0.80[AMR][1000 genomes]
rs1356748	0.82[CHB][hapmap]
rs2056304	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2139434	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34476793	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4633103	0.84[CHD][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap]
rs4871044	0.85[CHD][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap]
rs4871822	0.84[CHD][hapmap];0.83[MEX][hapmap]
rs58564644	0.80[AMR][1000 genomes]
rs60657932	0.80[AMR][1000 genomes]
rs6469889	0.82[CHB][hapmap];0.80[AMR][1000 genomes]
rs6469890	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs6980708	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs7817016	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7827219	0.84[CHD][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap]
rs7833689	0.82[CHB][hapmap];0.86[CHD][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes]
rs9643139	0.82[CHB][hapmap]

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	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1027974	chr8:120885478-121079658	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv539739	chr8:120885478-121079658	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv3348294	chr8:121000288-121250984	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4871827	SLC30A8	cis	cerebellum	SCAN
rs4871827	ATAD2	cis	parietal	SCAN
rs4871827	DSCC1	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:121017000-121067000	Weak transcription	Brain Anterior Caudate	brain
2	chr8:121022400-121065400	Weak transcription	Left Ventricle	heart
3	chr8:121036000-121063800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr8:121042000-121063400	Weak transcription	Spleen	Spleen
5	chr8:121046200-121065200	Weak transcription	Psoas Muscle	Psoas
6	chr8:121048800-121063600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr8:121048800-121063600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr8:121049200-121062200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr8:121049200-121072800	Weak transcription	Fetal Lung	lung
10	chr8:121049200-121072800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr8:121053600-121064000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr8:121053600-121067200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr8:121053600-121072800	Weak transcription	Brain Angular Gyrus	brain
14	chr8:121053600-121072800	Weak transcription	Brain Substantia Nigra	brain
15	chr8:121053600-121072800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr8:121053800-121072800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr8:121058400-121065400	Weak transcription	Pancreas	Pancrea
18	chr8:121058400-121066200	Weak transcription	Gastric	stomach
19	chr8:121059400-121077800	Weak transcription	Fetal Stomach	stomach
20	chr8:121059600-121064600	Weak transcription	Fetal Intestine Small	intestine
21	chr8:121060000-121062600	Enhancers	H1 Cell Line	embryonic stem cell
22	chr8:121060200-121062600	Enhancers	Liver	Liver
23	chr8:121060600-121063600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr8:121060600-121064400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr8:121060600-121085000	Weak transcription	Fetal Muscle Leg	muscle
26	chr8:121060800-121062200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr8:121060800-121063200	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr8:121060800-121072800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr8:121061000-121062600	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr8:121061000-121063000	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr8:121061000-121063000	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr8:121061000-121064000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr8:121061000-121064000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr8:121061000-121064200	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr8:121061000-121064600	Weak transcription	Ovary	ovary
36	chr8:121061000-121065400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr8:121061000-121072800	Weak transcription	Fetal Kidney	kidney
38	chr8:121061600-121064400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr8:121061600-121064600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr8:121061800-121062000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr8:121061800-121062000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr8:121061800-121062000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr8:121061800-121062200	Enhancers	H9 Cell Line	embryonic stem cell
44	chr8:121061800-121062200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr8:121061800-121062400	Strong transcription	Adipose Nuclei	Adipose
46	chr8:121061800-121062400	Strong transcription	Fetal Intestine Large	intestine
47	chr8:121061800-121062600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr8:121061800-121062600	Strong transcription	Colon Smooth Muscle	Colon
49	chr8:121061800-121063000	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr8:121061800-121063000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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