Variant report

Variant	rs9650616
Chromosome Location	chr8:8869199-8869200
allele	G/T
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	TBL1XR1	chr8:8869164-8870408	K562	blood:	n/a	n/a
2	IRF1	chr8:8867307-8870229	K562	blood:	n/a	chr8:8867842-8867853 chr8:8869776-8869785 chr8:8868594-8868614 chr8:8868056-8868070 chr8:8869777-8869786 chr8:8868054-8868068 chr8:8869449-8869460
3	POLR2A	chr8:8863320-8872107	K562	blood:	n/a	n/a
4	JUND	chr8:8868850-8869213	K562	blood:	n/a	n/a
5	ARID3A	chr8:8869067-8870052	K562	blood:	n/a	n/a
6	MAFK	chr8:8869042-8869819	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:8859472..8863506-chr8:8866779..8870820,4	MCF-7	breast:
2	chr8:8859158..8867027-chr8:8867199..8874373,17	K562	blood:
3	chr8:8748349..8752697-chr8:8864961..8869329,4	K562	blood:

Variant related genes	Relation type
ERI1	TF binding region
ENSG00000147324	Chromatin interaction
ENSG00000104626	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10217044	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045528	1.00[CHD][hapmap]
rs1045529	0.89[CEU][hapmap]
rs10503389	1.00[CHB][hapmap]
rs11784393	0.81[CEU][hapmap]
rs11785634	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11785819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11787026	0.93[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs12114954	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs13250919	1.00[CHD][hapmap]
rs13252797	1.00[CEU][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13271797	1.00[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13273769	1.00[CHD][hapmap]
rs1562211	0.81[CEU][hapmap]
rs17646349	1.00[CHB][hapmap]
rs17646897	1.00[CHB][hapmap]
rs17702602	0.89[CEU][hapmap]
rs2288671	0.85[CEU][hapmap]
rs2409120	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28482034	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28665409	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2915251	0.85[CEU][hapmap]
rs2956244	0.88[CEU][hapmap]
rs2979247	0.85[CEU][hapmap]
rs2979256	0.85[CEU][hapmap]
rs2979265	0.85[CEU][hapmap]
rs34004903	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34251783	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3855900	0.81[EUR][1000 genomes]
rs3895823	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4840389	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4841083	0.92[CEU][hapmap]
rs4841088	1.00[CHD][hapmap]
rs6601279	0.80[EUR][1000 genomes]
rs6601280	0.92[CEU][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs6601282	0.81[CEU][hapmap]
rs6748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6981060	0.80[EUR][1000 genomes]
rs6983877	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs6986044	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987107	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987558	0.85[CEU][hapmap]
rs7000799	1.00[CHB][hapmap]
rs7005056	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7005133	0.81[CEU][hapmap]
rs7017868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7814328	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9329175	0.96[CEU][hapmap];0.97[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][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
rs9650616	PPP1R3B	cis	cerebellum	SCAN
rs9650616	CTSB	cis	cerebellum	SCAN
rs9650616	DEFB134	cis	parietal	SCAN
rs9650616	THEX1	Cis_1M	lymphoblastoid	RTeQTL
rs9650616	DEFB134	cis	cerebellum	SCAN
rs9650616	MFHAS1	cis	cerebellum	SCAN

Chromatin state (count:121 , 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	chr8:8861600-8870600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr8:8861600-8876200	Weak transcription	Esophagus	oesophagus
5	chr8:8861600-8878600	Weak transcription	Colon Smooth Muscle	Colon
6	chr8:8861600-8885600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr8:8861800-8870400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr8:8861800-8870400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr8:8861800-8870400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr8:8861800-8870400	Weak transcription	Fetal Stomach	stomach
11	chr8:8861800-8870400	Weak transcription	Psoas Muscle	Psoas
12	chr8:8861800-8870600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr8:8861800-8870600	Weak transcription	Thymus	Thymus
14	chr8:8861800-8871000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr8:8861800-8871000	Weak transcription	HSMMtube	muscle
16	chr8:8861800-8871400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr8:8861800-8871600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr8:8861800-8874800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr8:8861800-8875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr8:8861800-8875000	Weak transcription	Gastric	stomach
21	chr8:8861800-8877800	Weak transcription	Right Ventricle	heart
22	chr8:8861800-8881800	Weak transcription	Fetal Kidney	kidney
23	chr8:8861800-8883400	Weak transcription	Spleen	Spleen
24	chr8:8861800-8883600	Weak transcription	Small Intestine	intestine
25	chr8:8861800-8885200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr8:8861800-8887200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr8:8861800-8887400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr8:8861800-8890000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr8:8861800-8891400	Weak transcription	Brain Angular Gyrus	brain
30	chr8:8861800-8891800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr8:8861800-8892000	Weak transcription	Brain Anterior Caudate	brain
32	chr8:8861800-8892200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr8:8861800-8892200	Weak transcription	Ovary	ovary
34	chr8:8861800-8893800	Weak transcription	Fetal Brain Male	brain
35	chr8:8861800-8897800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr8:8861800-8915600	Weak transcription	Pancreas	Pancrea
37	chr8:8862000-8869200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr8:8862000-8869600	Weak transcription	Fetal Lung	lung
39	chr8:8862000-8870400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr8:8862200-8870600	Weak transcription	Left Ventricle	heart
41	chr8:8862200-8870600	Weak transcription	Lung	lung
42	chr8:8862400-8874400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr8:8863400-8870800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr8:8864400-8870800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr8:8864600-8869800	Weak transcription	Stomach Mucosa	stomach
46	chr8:8864600-8870000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr8:8864600-8871000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr8:8864600-8871200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr8:8864800-8869400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr8:8864800-8869400	Weak transcription	Osteobl	bone

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