Variant report

Variant	rs6983708
Chromosome Location	chr8:52760365-52760366
allele	C/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	SETDB1	chr8:52760088-52760620	U2OS	brain:	n/a	n/a
2	FOS	chr8:52760331-52760475	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr8:52760326-52760513	MCF10A-Er-Src	breast:	n/a	n/a
4	FOXA2	chr8:52760142-52760454	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:52758813..52761713-chr8:52810752..52813685,2	MCF-7	breast:
2	chr8:52755886..52758501-chr8:52759669..52762301,2	MCF-7	breast:
3	chr8:52760042..52761761-chr8:52782452..52785170,2	K562	blood:

Variant related genes	Relation type
PCMTD1	TF binding region
ENSG00000168300	Chromatin interaction
ENSG00000228801	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10086425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10090429	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10094042	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10105030	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1013621	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1013622	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11774370	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11781801	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11782727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11786818	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12335014	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12677168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13249855	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13252779	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13252785	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13256197	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13263909	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13267241	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13268494	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13270008	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13275077	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13276858	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13279123	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1467197	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1515688	0.81[ASN][1000 genomes]
rs1517306	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16916858	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2176121	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2395826	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2395827	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28619907	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34619309	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35293585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4242474	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4242475	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4242476	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4285479	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4565453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4573263	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4587317	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4873611	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6473660	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6473667	0.88[ASN][1000 genomes]
rs6982622	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6986544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6988122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6990379	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7000135	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7001651	0.84[ASN][1000 genomes]
rs7004698	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7009748	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7013360	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7017926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs718251	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs722495	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7461587	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7462096	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7814421	0.87[ASN][1000 genomes]
rs7827298	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7827346	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7843189	0.85[ASN][1000 genomes]
rs925762	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9298462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][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	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv831316	chr8:52660353-52842928	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6983708	MED19	trans	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52722000-52771400	Weak transcription	Gastric	stomach
2	chr8:52731200-52763400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr8:52731200-52771000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr8:52733200-52763600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr8:52733200-52783800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr8:52733800-52776400	Weak transcription	GM12878-XiMat	blood
7	chr8:52734200-52761600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr8:52735600-52763600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr8:52735600-52773400	Weak transcription	Brain Germinal Matrix	brain
10	chr8:52735800-52763400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr8:52737200-52760400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:52739800-52765400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr8:52739800-52782600	Weak transcription	K562	blood
14	chr8:52742000-52765400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr8:52742600-52763400	Weak transcription	Brain Substantia Nigra	brain
16	chr8:52743000-52771400	Weak transcription	HepG2	liver
17	chr8:52743200-52765400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr8:52743400-52763400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr8:52743400-52766200	Weak transcription	HSMMtube	muscle
20	chr8:52743400-52771400	Weak transcription	Esophagus	oesophagus
21	chr8:52743800-52763000	Weak transcription	Fetal Kidney	kidney
22	chr8:52743800-52763600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr8:52743800-52765200	Weak transcription	Brain Hippocampus Middle	brain
24	chr8:52744000-52763000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr8:52744000-52763600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr8:52744000-52768200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr8:52744000-52771200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr8:52744000-52771400	Weak transcription	Fetal Brain Female	brain
29	chr8:52744200-52770800	Weak transcription	Placenta	Placenta
30	chr8:52744400-52768600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr8:52744600-52762400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr8:52744600-52769000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr8:52744600-52769200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr8:52745600-52768200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr8:52745800-52762600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr8:52745800-52765400	Weak transcription	Thymus	Thymus
37	chr8:52745800-52769400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr8:52746000-52762200	Weak transcription	Liver	Liver
39	chr8:52746000-52763000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr8:52746000-52765600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr8:52746200-52762400	Weak transcription	Adipose Nuclei	Adipose
42	chr8:52746200-52763000	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr8:52751000-52765400	Weak transcription	Fetal Intestine Large	intestine
44	chr8:52751000-52765400	Weak transcription	Fetal Stomach	stomach
45	chr8:52751000-52768000	Weak transcription	Fetal Muscle Leg	muscle
46	chr8:52751200-52765400	Weak transcription	Fetal Intestine Small	intestine
47	chr8:52751200-52771400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr8:52752000-52763600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr8:52752400-52762400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr8:52752400-52763000	Weak transcription	Primary B cells from peripheral blood	blood

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