Variant report

Variant	rs62112163
Chromosome Location	chr19:36275074-36275075
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	chr19:36274956-36275312	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36273554..36275666-chr19:36279715..36282125,2	MCF-7	breast:
2	chr19:36248580..36254743-chr19:36274692..36280659,6	K562	blood:
3	chr19:36248761..36250845-chr19:36272724..36275459,2	MCF-7	breast:

Variant related genes	Relation type
ARHGAP33	TF binding region
ENSG00000167595	Chromatin interaction
ENSG00000004776	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11084829	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1133745	0.81[ASN][1000 genomes]
rs11671256	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11671985	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12460977	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2291067	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35627066	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3925318	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3933421	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56003270	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59805670	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61544275	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62112162	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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	191 gene(s)	inside rSNPs	diseases
2	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv911633	chr19:36206050-36283847	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
6	nsv911634	chr19:36206050-36290977	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
7	nsv1057830	chr19:36210269-36279794	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	nsv543997	chr19:36210269-36279794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	nsv911635	chr19:36217333-36283847	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv458567	chr19:36221051-36283847	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
11	nsv579423	chr19:36221051-36283847	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv911636	chr19:36240960-36290977	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	nsv911637	chr19:36261928-36309321	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
14	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs62112163	U2AF1L4	Cis_1M	lymphoblastoid	RTeQTL
rs62112163	TMEM149	Cis_1M	lymphoblastoid	RTeQTL
rs62112163	TMEM149	cis	multi-tissue	Pritchard
rs62112163	U2AF1L4	cis	Muscle Skeletal	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36266800-36281800	Weak transcription	Liver	Liver
2	chr19:36267400-36275200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr19:36267400-36275400	Weak transcription	Primary B cells from cord blood	blood
4	chr19:36267400-36276000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr19:36267400-36276000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr19:36267400-36277600	Weak transcription	Right Atrium	heart
7	chr19:36267400-36277800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:36267400-36281600	Weak transcription	Small Intestine	intestine
9	chr19:36267600-36275400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr19:36267600-36279200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr19:36267800-36276400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr19:36267800-36278000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr19:36267800-36280600	Weak transcription	HUVEC	blood vessel
14	chr19:36267800-36284200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:36268000-36275200	Weak transcription	Colon Smooth Muscle	Colon
16	chr19:36268400-36278600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:36268400-36278600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:36268400-36284200	Weak transcription	K562	blood
19	chr19:36268600-36277600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr19:36268600-36279200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr19:36268600-36279400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:36268600-36279600	Strong transcription	Thymus	Thymus
23	chr19:36268600-36281000	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr19:36268600-36281000	Strong transcription	Fetal Stomach	stomach
25	chr19:36268800-36277800	Strong transcription	Fetal Muscle Trunk	muscle
26	chr19:36268800-36278400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr19:36268800-36278600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:36268800-36278800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:36268800-36279000	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr19:36268800-36280000	Strong transcription	Fetal Muscle Leg	muscle
31	chr19:36269000-36275600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr19:36269000-36277800	Strong transcription	Fetal Thymus	thymus
33	chr19:36269000-36278400	Strong transcription	Lung	lung
34	chr19:36269000-36278800	Strong transcription	Brain Hippocampus Middle	brain
35	chr19:36269200-36277200	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr19:36269200-36279200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr19:36269400-36278400	Strong transcription	Spleen	Spleen
38	chr19:36269600-36276800	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr19:36270000-36277400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr19:36270000-36278400	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr19:36270200-36278400	Strong transcription	Dnd41	blood
42	chr19:36270400-36278200	Weak transcription	Fetal Brain Male	brain
43	chr19:36271000-36277600	Strong transcription	Aorta	Aorta
44	chr19:36271000-36281200	Strong transcription	Brain Germinal Matrix	brain
45	chr19:36271000-36281200	Strong transcription	Fetal Brain Female	brain
46	chr19:36271400-36277400	Strong transcription	NHLF	lung
47	chr19:36271600-36276600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:36272200-36281000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:36272400-36276600	Weak transcription	Primary T cells from cord blood	blood
50	chr19:36272600-36276000	Weak transcription	Placenta	Placenta

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