Variant report

Variant	rs11711407
Chromosome Location	chr3:50225029-50225030
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	POLR2A	chr3:50224990-50225186	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:50193362..50195902-chr3:50224405..50227347,2	K562	blood:
2	chr3:50153449..50156206-chr3:50223534..50226220,2	K562	blood:
3	chr3:50157801..50161419-chr3:50224013..50228566,6	MCF-7	breast:
4	chr3:50224996..50226942-chr3:50236874..50238990,2	K562	blood:

Variant related genes	Relation type
GNAT1	TF binding region
ENSG00000235016	Chromatin interaction
ENSG00000003756	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11714286	0.84[EUR][1000 genomes]
rs11714799	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717349	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12631337	0.89[EUR][1000 genomes]
rs13085567	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1858828	0.82[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2073726	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236942	0.96[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2282749	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34877766	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3755831	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3774745	0.81[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3774749	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3774750	0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3774751	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4688745	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67627084	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9831967	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9858059	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv876768	chr3:50144951-50267584	Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription 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 miRNA target site	94 gene(s)	inside rSNPs	diseases
9	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
10	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
11	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
12	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
13	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
14	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
15	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
16	nsv460529	chr3:50178011-50324672	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
17	nsv460530	chr3:50178011-50324672	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
18	nsv590252	chr3:50178011-50324672	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
19	nsv1002916	chr3:50187646-50311666	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
20	nsv536564	chr3:50187646-50311666	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
21	nsv1014256	chr3:50187646-50339163	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS 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 miRNA target site	53 gene(s)	inside rSNPs	diseases
22	nsv536565	chr3:50187646-50339163	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Genic enhancers 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 miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
23	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
24	nsv590253	chr3:50196418-50337422	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
25	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
26	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
27	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs11711407	RBM6	cis	cerebellum	SCAN
rs11711407	RNF123	cis	cerebellum	SCAN
rs11711407	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs11711407	RBM6	cis	Esophagus Muscularis	GTEx
rs11711407	RBM6	cis	Nerve Tibial	GTEx
rs11711407	RBM6	cis	Heart Left Ventricle	GTEx
rs11711407	HYAL3	cis	multi-tissue	Pritchard
rs11711407	RBM6	cis	multi-tissue	Pritchard
rs11711407	RNF123	cis	parietal	SCAN
rs11711407	PTH1R	cis	parietal	SCAN
rs11711407	RBM6	cis	Thyroid	GTEx
rs11711407	RBM6	cis	Artery Aorta	GTEx
rs11711407	RBM6	cis	lymphoblastoid	seeQTL
rs11711407	RBM6	cis	Artery Tibial	GTEx
rs11711407	RBM6	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50204600-50226600	Weak transcription	Brain Anterior Caudate	brain
2	chr3:50205400-50226600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:50205400-50226600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:50206400-50226600	Weak transcription	NHLF	lung
5	chr3:50208800-50226600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:50208800-50226600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:50208800-50226600	Weak transcription	Osteobl	bone
8	chr3:50210400-50229200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:50210400-50242400	Weak transcription	Right Atrium	heart
10	chr3:50210600-50229400	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:50211400-50230400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:50212200-50226600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:50213600-50226400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:50214200-50230600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:50215000-50226600	Weak transcription	HSMMtube	muscle
16	chr3:50216600-50226200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:50217000-50226000	Strong transcription	NHEK	skin
18	chr3:50218000-50225600	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr3:50218000-50226200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:50218000-50226200	Weak transcription	Stomach Mucosa	stomach
21	chr3:50218000-50228600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:50218800-50226200	Strong transcription	Brain Germinal Matrix	brain
23	chr3:50219000-50225800	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr3:50219200-50226000	Strong transcription	Fetal Brain Female	brain
25	chr3:50219200-50226200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:50219200-50226400	Strong transcription	Fetal Stomach	stomach
27	chr3:50219400-50225400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr3:50219400-50225400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr3:50219400-50226000	Strong transcription	Lung	lung
30	chr3:50219400-50226200	Strong transcription	Adipose Nuclei	Adipose
31	chr3:50219400-50226600	Strong transcription	HMEC	breast
32	chr3:50219600-50225800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:50219600-50226000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:50219600-50226000	Strong transcription	Spleen	Spleen
35	chr3:50219800-50225200	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:50219800-50226000	Strong transcription	Fetal Muscle Leg	muscle
37	chr3:50220000-50231800	Weak transcription	K562	blood
38	chr3:50220200-50225600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr3:50220200-50228400	Weak transcription	HUVEC	blood vessel
40	chr3:50220400-50226000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:50220400-50228400	Weak transcription	Hela-S3	cervix
42	chr3:50220600-50226600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:50220800-50225400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:50220800-50230200	Weak transcription	Colonic Mucosa	Colon
45	chr3:50221200-50225200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr3:50221400-50225400	Strong transcription	Fetal Lung	lung
47	chr3:50221600-50228400	Weak transcription	HepG2	liver
48	chr3:50222000-50226400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:50222200-50225200	Genic enhancers	Placenta	Placenta
50	chr3:50222200-50226000	Strong transcription	Gastric	stomach

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