Variant report

Variant	rs61876202
Chromosome Location	chr11:8854673-8854674
allele	A/C
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	TCF3	chr11:8854409-8854795	GM12878	blood:	n/a	chr11:8854558-8854568
2	STAT1	chr11:8853916-8854879	Hela-S3	cervix:	n/a	chr11:8854224-8854235 chr11:8854223-8854237 chr11:8854569-8854578 chr11:8854226-8854234 chr11:8854568-8854577
3	RUNX3	chr11:8854223-8854900	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:8854283-8854731	GM12878	blood:	n/a	n/a
5	STAT3	chr11:8853913-8855864	MCF10A-Er-Src	breast:	n/a	chr11:8854223-8854237 chr11:8854569-8854578 chr11:8854226-8854234 chr11:8854568-8854577
6	EP300	chr11:8854408-8854813	SK-N-SH_RA	brain:	n/a	n/a
7	PAX5	chr11:8854430-8854866	GM12891	blood:	n/a	chr11:8854702-8854711
8	RCOR1	chr11:8854006-8854903	IMR90	lung:	n/a	n/a
9	NFE2	chr11:8854567-8854681	GM12878	blood:	n/a	n/a
10	STAT3	chr11:8854010-8856009	MCF10A-Er-Src	breast:	n/a	chr11:8854223-8854237 chr11:8854569-8854578 chr11:8854226-8854234 chr11:8854568-8854577
11	MTA3	chr11:8854083-8854899	GM12878	blood:	n/a	n/a
12	RELA	chr11:8854077-8854880	GM12891	blood:	n/a	n/a
13	MAX	chr11:8854177-8854820	GM12878	blood:	n/a	n/a
14	YY1	chr11:8854428-8854822	GM12892	blood:	n/a	n/a
15	IKZF1	chr11:8854258-8854914	GM12878	blood:	n/a	n/a
16	PAX5	chr11:8854462-8854867	GM12878	blood:	n/a	chr11:8854702-8854711
17	MYC	chr11:8854023-8854853	MCF10A-Er-Src	breast:	n/a	n/a
18	EP300	chr11:8854539-8855038	GM12878	blood:	n/a	chr11:8854933-8854941
19	TAF1	chr11:8854442-8854711	GM12892	blood:	n/a	n/a
20	STAT3	chr11:8854020-8855893	MCF10A-Er-Src	breast:	n/a	chr11:8854223-8854237 chr11:8854569-8854578 chr11:8854226-8854234 chr11:8854568-8854577
21	MAZ	chr11:8854389-8854721	GM12878	blood:	n/a	n/a
22	CTCF	chr11:8854381-8854748	GM12878	blood:	n/a	n/a
23	TBL1XR1	chr11:8854332-8854817	GM12878	blood:	n/a	n/a
24	EBF1	chr11:8854464-8854776	GM12878	blood:	n/a	n/a
25	NFIC	chr11:8854303-8855395	GM12878	blood:	n/a	n/a
26	TCF12	chr11:8854423-8854862	GM12878	blood:	n/a	n/a
27	POLR2A	chr11:8854369-8854699	GM12878	blood:	n/a	n/a
28	YY1	chr11:8854357-8854811	GM12878	blood:	n/a	n/a
29	PAX5	chr11:8854515-8854799	GM12892	blood:	n/a	chr11:8854702-8854711
30	TCF3	chr11:8854427-8854885	GM12878	blood:	n/a	chr11:8854558-8854568
31	TCF12	chr11:8854468-8854837	GM12878	blood:	n/a	n/a
32	RAD21	chr11:8854373-8854828	SK-N-SH_RA	brain:	n/a	n/a
33	PAX5	chr11:8854532-8854787	GM12892	blood:	n/a	chr11:8854702-8854711
34	POLR2A	chr11:8854193-8854865	GM12892	blood:	n/a	n/a
35	TCF12	chr11:8853894-8855032	SK-N-SH	brain:	n/a	n/a
36	EBF1	chr11:8854235-8854837	GM12878	blood:	n/a	n/a
37	FOS	chr11:8854057-8854802	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr11:8854305-8854808	GM12892	blood:	n/a	n/a
39	FOXM1	chr11:8854258-8855010	GM12878	blood:	n/a	n/a
40	POLR2A	chr11:8854386-8854795	GM12878	blood:	n/a	n/a
41	RELA	chr11:8854206-8854898	GM19099	blood:	n/a	n/a
42	POLR2A	chr11:8854056-8854863	GM12878	blood:	n/a	n/a
43	POLR2A	chr11:8854090-8854880	GM12892	blood:	n/a	n/a
44	PML	chr11:8854032-8854894	GM12878	blood:	n/a	n/a
45	RELA	chr11:8854417-8854872	GM19193	blood:	n/a	n/a
46	YY1	chr11:8854388-8854789	SK-N-SH_RA	brain:	n/a	n/a
47	PAX5	chr11:8854208-8854897	GM12878	blood:	n/a	chr11:8854702-8854711
48	SMC3	chr11:8854270-8854741	GM12878	blood:	n/a	n/a
49	ATF2	chr11:8854357-8854917	GM12878	blood:	n/a	n/a
50	MAX	chr11:8854011-8854855	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8840012..8842971-chr11:8854220..8856402,2	MCF-7	breast:

Variant related genes	Relation type
ST5	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10743091	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10840135	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10840137	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11042097	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11042098	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11042104	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12798322	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1368017	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16906256	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2292049	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2568025	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2568031	0.82[AMR][1000 genomes]
rs2568032	0.81[AMR][1000 genomes]
rs34874636	0.86[AMR][1000 genomes]
rs59025804	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7127479	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7948452	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv527920	chr11:8816695-8856822	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs61876202	TMEM9B	Cis_1M	lymphoblastoid	RTeQTL
rs61876202	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs61876202	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs61876202	TMEM9B-AS1	cis	lung	GTEx
rs61876202	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx
rs61876202	TMEM9B-AS1	cis	Thyroid	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8833200-8859800	Weak transcription	Aorta	Aorta
2	chr11:8845800-8860000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr11:8851000-8859200	Weak transcription	Fetal Lung	lung
4	chr11:8851000-8861400	Weak transcription	Brain Substantia Nigra	brain
5	chr11:8851600-8856200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:8851800-8862400	Enhancers	Placenta	Placenta
7	chr11:8852000-8859200	Enhancers	Placenta Amnion	Placenta Amnion
8	chr11:8852600-8855400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:8852600-8856200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:8852600-8856400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:8852800-8854800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:8852800-8855800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:8852800-8861600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr11:8853000-8856200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr11:8853000-8856200	Enhancers	HMEC	breast
16	chr11:8853000-8856400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:8853000-8856400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr11:8853000-8858000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:8853000-8861400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr11:8853400-8854800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:8853400-8856000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr11:8853400-8856000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:8853400-8856200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:8853400-8856400	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr11:8853400-8857600	Enhancers	NHLF	lung
26	chr11:8853600-8854800	Flanking Active TSS	NHEK	skin
27	chr11:8853600-8855400	Enhancers	Esophagus	oesophagus
28	chr11:8853600-8855800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr11:8853600-8856200	Enhancers	Colon Smooth Muscle	Colon
30	chr11:8853600-8856800	Enhancers	NH-A	brain
31	chr11:8853800-8854800	Enhancers	Fetal Thymus	thymus
32	chr11:8853800-8856400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr11:8853800-8856400	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr11:8853800-8856400	Enhancers	Fetal Muscle Leg	muscle
35	chr11:8854000-8854800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr11:8854000-8854800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr11:8854000-8855600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr11:8854000-8855600	Enhancers	Fetal Heart	heart
39	chr11:8854000-8855600	Enhancers	Left Ventricle	heart
40	chr11:8854000-8855600	Enhancers	Hela-S3	cervix
41	chr11:8854000-8855800	Enhancers	Primary B cells from peripheral blood	blood
42	chr11:8854000-8855800	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr11:8854000-8856000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr11:8854000-8856000	Enhancers	Dnd41	blood
45	chr11:8854000-8856200	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr11:8854000-8856400	Enhancers	H1 Cell Line	embryonic stem cell
47	chr11:8854000-8856400	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr11:8854000-8856400	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr11:8854000-8856400	Enhancers	Osteobl	bone
50	chr11:8854200-8854800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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