Variant report

Variant	rs7853
Chromosome Location	chr8:8890814-8890815
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:8890241..8892505-chr8:9006726..9010652,3	MCF-7	breast:
2	chr8:8886740..8888994-chr8:8890137..8892927,2	K562	blood:

Variant related genes	Relation type
ENSG00000173281	Chromatin interaction
ENSG00000253426	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1045529	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11782281	0.85[ASN][1000 genomes]
rs11784393	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13272451	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1562211	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2044387	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2288671	0.84[EUR][1000 genomes]
rs2288673	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2915251	0.85[EUR][1000 genomes]
rs2921378	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2921383	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2953805	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2953806	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2956244	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2979247	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2979253	0.93[AMR][1000 genomes]
rs2979256	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2979265	0.87[EUR][1000 genomes]
rs3021416	0.91[AMR][1000 genomes]
rs4537305	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4841083	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4841084	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6987558	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6993244	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7005133	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7016139	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7813388	0.95[ASN][1000 genomes]
rs7824140	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv831229	chr8:8751523-8926235	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv610205	chr8:8799111-8891644	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	n/a
5	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7853	SGK223	cis	Thyroid	GTEx
rs7853	C8orf5	Cis_chr	lymphoblastoid	RTeQTL
rs7853	RP11-62H7.2	cis	Thyroid	GTEx
rs7853	RP11-62H7.2	cis	Stomach	GTEx
rs7853	THEX1	Cis_1M	lymphoblastoid	RTeQTL
rs7853	BLK	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8861200-8892400	Weak transcription	Aorta	Aorta
2	chr8:8861400-8907000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr8:8861800-8891400	Weak transcription	Brain Angular Gyrus	brain
4	chr8:8861800-8891800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr8:8861800-8892000	Weak transcription	Brain Anterior Caudate	brain
6	chr8:8861800-8892200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr8:8861800-8892200	Weak transcription	Ovary	ovary
8	chr8:8861800-8893800	Weak transcription	Fetal Brain Male	brain
9	chr8:8861800-8897800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr8:8861800-8915600	Weak transcription	Pancreas	Pancrea
11	chr8:8870600-8892200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr8:8871200-8900000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr8:8871400-8892800	Weak transcription	HSMMtube	muscle
14	chr8:8871800-8894400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr8:8872000-8891200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr8:8875000-8891200	Weak transcription	Fetal Intestine Small	intestine
17	chr8:8875200-8897200	Weak transcription	Gastric	stomach
18	chr8:8875400-8892600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr8:8875400-8894400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr8:8875400-8897000	Weak transcription	Lung	lung
21	chr8:8875400-8901200	Weak transcription	Thymus	Thymus
22	chr8:8875800-8892200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr8:8876400-8898000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr8:8876800-8891400	Weak transcription	Fetal Brain Female	brain
25	chr8:8877000-8894600	Weak transcription	HMEC	breast
26	chr8:8877000-8895600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr8:8877000-8903400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr8:8877200-8895400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr8:8879200-8892600	Weak transcription	Osteobl	bone
30	chr8:8879400-8894200	Weak transcription	HepG2	liver
31	chr8:8881000-8900400	Weak transcription	NH-A	brain
32	chr8:8881200-8892000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr8:8881600-8891400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr8:8882200-8896400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr8:8882600-8894600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr8:8882600-8894600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr8:8883000-8893200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr8:8883200-8898400	Weak transcription	Fetal Kidney	kidney
39	chr8:8883600-8902400	Weak transcription	Adipose Nuclei	Adipose
40	chr8:8883800-8891000	Weak transcription	Stomach Mucosa	stomach
41	chr8:8883800-8892200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr8:8883800-8893800	Weak transcription	NHDF-Ad	bronchial
43	chr8:8883800-8895400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr8:8883800-8897800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr8:8883800-8906000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr8:8884000-8891200	Weak transcription	HUVEC	blood vessel
47	chr8:8884000-8891400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr8:8884000-8892400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr8:8884000-8894400	Weak transcription	Fetal Heart	heart
50	chr8:8884000-8895000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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