Variant report

Variant	rs6601694
Chromosome Location	chr8:8248058-8248059
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	MAX	chr8:8247825-8248190	GM12878	blood:	n/a	n/a
2	ATF2	chr8:8247266-8248601	GM12878	blood:	n/a	n/a
3	EBF1	chr8:8247488-8248470	GM12878	blood:	n/a	chr8:8248230-8248241
4	KAP1	chr8:8247588-8248863	U2OS	brain:	n/a	n/a
5	RUNX3	chr8:8247417-8248547	GM12878	blood:	n/a	n/a
6	FOXM1	chr8:8247347-8248604	GM12878	blood:	n/a	n/a
7	MTA3	chr8:8247396-8248522	GM12878	blood:	n/a	n/a
8	EP300	chr8:8247971-8248471	GM12878	blood:	n/a	n/a
9	WRNIP1	chr8:8247866-8248210	GM12878	blood:	n/a	n/a
10	IKZF1	chr8:8247789-8248504	GM12878	blood:	n/a	n/a
11	RUNX3	chr8:8247318-8248655	GM12878	blood:	n/a	n/a
12	IRF4	chr8:8247430-8248472	GM12878	blood:	n/a	n/a
13	RELA	chr8:8247474-8248548	GM15510	blood:	n/a	chr8:8247612-8247621 chr8:8247612-8247621
14	EBF1	chr8:8248000-8248474	GM12878	blood:	n/a	chr8:8248230-8248241
15	BATF	chr8:8248010-8248462	GM12878	blood:	n/a	n/a
16	GATA2	chr8:8247700-8248122	SH-SY5Y	brain:	n/a	n/a
17	RELA	chr8:8247428-8248679	GM18505	blood:	n/a	chr8:8247612-8247621 chr8:8247612-8247621
18	NFIC	chr8:8247227-8248647	GM12878	blood:	n/a	chr8:8247607-8247635
19	BCL11A	chr8:8248056-8248500	GM12878	blood:	n/a	n/a
20	MTA3	chr8:8247244-8248605	GM12878	blood:	n/a	n/a
21	STAT5A	chr8:8247478-8248478	GM12878	blood:	n/a	n/a
22	RELA	chr8:8247432-8248456	GM12878	blood:	n/a	chr8:8247612-8247621 chr8:8247612-8247621
23	BCL3	chr8:8248024-8248457	GM12878	blood:	n/a	n/a
24	KAP1	chr8:8246576-8248773	HEK293	kidney:	n/a	n/a
25	MAZ	chr8:8247985-8248340	GM12878	blood:	n/a	n/a
26	RELA	chr8:8247443-8248510	GM18951	blood:	n/a	chr8:8247612-8247621 chr8:8247612-8247621
27	MEF2A	chr8:8248056-8248462	GM12878	blood:	n/a	n/a
28	BATF	chr8:8248034-8248454	GM12878	blood:	n/a	n/a
29	RELA	chr8:8247429-8248621	GM12891	blood:	n/a	chr8:8247612-8247621 chr8:8247612-8247621
30	RELA	chr8:8248030-8248443	GM19099	blood:	n/a	n/a
31	ATF2	chr8:8247278-8248517	GM12878	blood:	n/a	n/a
32	STAT3	chr8:8248007-8248351	GM12878	blood:	n/a	n/a
33	NFIC	chr8:8247908-8248809	GM12878	blood:	n/a	n/a
34	GATA3	chr8:8247678-8248261	SH-SY5Y	brain:	n/a	n/a
35	TBL1XR1	chr8:8247573-8248410	GM12878	blood:	n/a	n/a
36	EBF1	chr8:8247983-8248426	GM12878	blood:	n/a	chr8:8248230-8248241

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRAGMIN.1-5	chr8:8247672-8248105	FPKM1_group_30826_transcript_2
2	lnc-PRAGMIN.1-5	chr8:8247672-8248105	NONHSAT124872

Variant related genes	Relation type
ENSG00000182319	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12680219	0.83[GIH][hapmap]
rs17669947	0.83[GIH][hapmap]
rs35520190	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817196	chr8:8079861-8255544	Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	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
3	nsv465448	chr8:8098079-8403142	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv610152	chr8:8098079-8403142	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv610153	chr8:8098079-8454531	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv610154	chr8:8101641-8328101	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1020290	chr8:8108863-8260280	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv539440	chr8:8108863-8260280	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1025994	chr8:8108863-8580201	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv1029268	chr8:8130629-8403435	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv539446	chr8:8130629-8403435	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1030433	chr8:8130629-8653691	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	nsv539447	chr8:8130629-8653691	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv831227	chr8:8204838-8367160	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv1033463	chr8:8221922-8674333	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
16	nsv539451	chr8:8221922-8674333	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
17	nsv1019613	chr8:8239352-8636357	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv539452	chr8:8239352-8636357	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	esv33063	chr8:8247056-8249234	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6601694	MTMR9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8244600-8248800	Weak transcription	Ovary	ovary
2	chr8:8244600-8249600	Weak transcription	Right Atrium	heart
3	chr8:8244800-8248200	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr8:8245000-8248200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr8:8245000-8248200	Enhancers	Primary B cells from peripheral blood	blood
6	chr8:8245000-8249200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr8:8245000-8255600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr8:8245000-8256800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:8245200-8248400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr8:8245400-8249400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr8:8245600-8248200	Weak transcription	Placenta	Placenta
12	chr8:8246600-8248400	Enhancers	H1 Cell Line	embryonic stem cell
13	chr8:8246600-8248800	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr8:8246600-8249000	Enhancers	Placenta Amnion	Placenta Amnion
15	chr8:8246600-8249400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr8:8246800-8249000	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr8:8246800-8249400	Enhancers	H9 Cell Line	embryonic stem cell
18	chr8:8247000-8248200	Enhancers	HepG2	liver
19	chr8:8247200-8249600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr8:8247400-8248400	Flanking Active TSS	GM12878-XiMat	blood
21	chr8:8247400-8249400	Enhancers	Duodenum Mucosa	Duodenum
22	chr8:8247400-8250000	Enhancers	Fetal Intestine Large	intestine
23	chr8:8247800-8248200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr8:8247800-8248200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr8:8247800-8248200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr8:8247800-8248200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr8:8247800-8248400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr8:8248000-8248600	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr8:8248000-8249400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr8:8248000-8249400	Enhancers	Fetal Intestine Small	intestine
31	chr8:8248000-8254400	Weak transcription	Fetal Kidney	kidney

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