Variant report

Variant	rs6960317
Chromosome Location	chr7:102793551-102793552
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	POLR2A	chr7:102793138-102793759	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:102784051..102785716-chr7:102793385..102795157,2	K562	blood:
2	chr7:102759379..102762894-chr7:102787802..102793821,6	K562	blood:
3	chr7:102789269..102791743-chr7:102791840..102795059,5	MCF-7	breast:

Variant related genes	Relation type
NAPEPLD	TF binding region
ENSG00000236848	TF binding region
ENSG00000161048	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10234363	0.84[EUR][1000 genomes]
rs10242349	0.84[EUR][1000 genomes]
rs10249921	0.84[EUR][1000 genomes]
rs10279441	0.84[EUR][1000 genomes]
rs17136070	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17156420	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs1968196	0.88[EUR][1000 genomes]
rs1968197	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs28397594	0.91[EUR][1000 genomes]
rs28675125	0.84[EUR][1000 genomes]
rs3864442	0.88[EUR][1000 genomes]
rs3959192	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4727568	0.82[MKK][hapmap]
rs57770439	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58202498	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58418722	0.84[EUR][1000 genomes]
rs58443652	0.91[EUR][1000 genomes]
rs59245803	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60020835	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60080018	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60366734	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60383417	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6975450	0.82[EUR][1000 genomes]
rs6978467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6978540	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6978608	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6979451	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7789727	1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs7801094	0.93[EUR][1000 genomes]
rs7810936	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv831084	chr7:102778908-102964970	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv966872	chr7:102791751-102798505	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6960317	POLR2J	cis	multi-tissue	Pritchard

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102790200-102793600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:102790200-102793600	Enhancers	HepG2	liver
3	chr7:102790200-102803200	Weak transcription	Gastric	stomach
4	chr7:102790400-102793600	Enhancers	Fetal Intestine Small	intestine
5	chr7:102790400-102794000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:102790400-102794000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr7:102790400-102796800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:102790800-102795600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr7:102790800-102795800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:102790800-102795800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr7:102790800-102796200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr7:102791000-102794000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr7:102791000-102795600	Weak transcription	Brain Substantia Nigra	brain
14	chr7:102791000-102795800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr7:102791000-102795800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr7:102791000-102795800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr7:102791000-102796200	Weak transcription	Spleen	Spleen
18	chr7:102791200-102794000	Weak transcription	GM12878-XiMat	blood
19	chr7:102791200-102794200	Enhancers	Fetal Intestine Large	intestine
20	chr7:102791200-102794800	Enhancers	K562	blood
21	chr7:102792200-102796000	Weak transcription	Small Intestine	intestine
22	chr7:102792400-102794600	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr7:102792600-102794000	Weak transcription	Stomach Mucosa	stomach
24	chr7:102793000-102794400	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr7:102793200-102793800	Active TSS	Duodenum Mucosa	Duodenum
26	chr7:102793200-102794200	Active TSS	Brain Hippocampus Middle	brain
27	chr7:102793200-102794400	Enhancers	Colonic Mucosa	Colon
28	chr7:102793200-102794600	Active TSS	Brain Anterior Caudate	brain
29	chr7:102793400-102794000	Active TSS	Liver	Liver
30	chr7:102793400-102794200	Active TSS	Brain Cingulate Gyrus	brain
31	chr7:102793400-102796000	Weak transcription	Rectal Mucosa Donor 29	rectum

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