Variant report

Variant	rs3826993
Chromosome Location	chr19:19250145-19250146
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr19:19249066-19250742	U2OS	brain:	n/a	n/a
2	HCFC1	chr19:19248492-19251341	Hela-S3	cervix:	n/a	n/a
3	RCOR1	chr19:19248766-19251323	IMR90	lung:	n/a	n/a
4	RPC155	chr19:19249852-19250727	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr19:19250060-19250210	HPAF	blood vessel:	n/a	n/a
6	CTCF	chr19:19250040-19250190	NHDF-neo	bronchial:	n/a	n/a
7	CTCF	chr19:19250040-19250190	SAEC	small airway:	n/a	n/a
8	CTCF	chr19:19250000-19250150	HUVEC	blood vessel:	n/a	n/a
9	CTCF	chr19:19250000-19250150	HepG2	liver:	n/a	n/a
10	CTCF	chr19:19249893-19250923	A549	lung:	n/a	chr19:19250619-19250635
11	CTCF	chr19:19250000-19250150	AoAF	blood vessel:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19250055..19252168-chr19:19339457..19341497,2	K562	blood:
2	chr19:19164361..19165421-chr19:19250084..19251151,9	MCF-7	breast:
3	chr19:19110446..19112706-chr19:19249523..19251357,2	K562	blood:
4	chr19:19172595..19175925-chr19:19247411..19251399,4	MCF-7	breast:
5	chr19:19249614..19251216-chr19:19284548..19287281,2	K562	blood:
6	chr19:19163970..19165547-chr19:19250085..19250832,6	MCF-7	breast:
7	chr19:19229446..19234006-chr19:19241302..19251526,15	K562	blood:
8	chr19:19164345..19165259-chr19:19250077..19251091,6	K562	blood:
9	chr19:19165793..19166709-chr19:19249860..19250614,2	MCF-7	breast:
10	chr19:19169646..19176603-chr19:19241603..19250623,23	K562	blood:
11	chr19:19164507..19166528-chr19:19249184..19251105,2	K562	blood:
12	chr19:19239875..19242628-chr19:19248589..19251207,2	MCF-7	breast:
13	chr19:19231565..19233843-chr19:19248127..19250421,2	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM161A	TF binding region
ENSG00000105676	Chromatin interaction
ENSG00000064545	Chromatin interaction
ENSG00000064607	Chromatin interaction
ENSG00000181035	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10414676	0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs2040561	0.90[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2040562	0.91[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3826994	0.90[CHB][hapmap]
rs4808924	0.81[EUR][1000 genomes]
rs6511020	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6511021	0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs964132	0.85[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3826993	TMEM161A	cis	Muscle Skeletal	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19249200-19256600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:19249400-19250600	Enhancers	Primary T cells fromperipheralblood	blood
3	chr19:19249400-19250600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:19249400-19250600	Weak transcription	Placenta	Placenta
5	chr19:19249400-19250600	Enhancers	Fetal Thymus	thymus
6	chr19:19249400-19250800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:19249400-19250800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr19:19249400-19250800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr19:19249400-19250800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:19249400-19256600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:19249400-19256800	Weak transcription	Lung	lung
12	chr19:19249400-19257400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:19249400-19259600	Weak transcription	Aorta	Aorta
14	chr19:19249400-19259800	Weak transcription	Left Ventricle	heart
15	chr19:19249400-19271200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:19249600-19250400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:19249600-19250600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:19249600-19250800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:19249600-19250800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr19:19249600-19250800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:19249600-19250800	Enhancers	Primary B cells from peripheral blood	blood
22	chr19:19249600-19251200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr19:19249600-19253000	Weak transcription	Liver	Liver
24	chr19:19249600-19256800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:19249600-19257400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr19:19249600-19257600	Weak transcription	Brain Hippocampus Middle	brain
27	chr19:19249600-19258400	Weak transcription	Right Atrium	heart
28	chr19:19249600-19271800	Weak transcription	Brain Substantia Nigra	brain
29	chr19:19249600-19282600	Weak transcription	NHLF	lung
30	chr19:19249800-19250200	Active TSS	Brain Cingulate Gyrus	brain
31	chr19:19249800-19250200	Enhancers	Brain Germinal Matrix	brain
32	chr19:19249800-19250400	Weak transcription	Thymus	Thymus
33	chr19:19249800-19250600	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr19:19249800-19250600	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr19:19249800-19250600	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr19:19249800-19250600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr19:19249800-19250600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr19:19249800-19256600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr19:19249800-19256800	Weak transcription	Ovary	ovary
40	chr19:19249800-19256800	Weak transcription	K562	blood
41	chr19:19249800-19256800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr19:19249800-19257200	Weak transcription	GM12878-XiMat	blood
43	chr19:19249800-19257400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:19249800-19257400	Weak transcription	Colon Smooth Muscle	Colon
45	chr19:19249800-19257400	Weak transcription	Spleen	Spleen
46	chr19:19249800-19258400	Weak transcription	Dnd41	blood
47	chr19:19249800-19258800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:19249800-19259600	Weak transcription	Primary T cells from cord blood	blood
49	chr19:19249800-19259800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr19:19249800-19260000	Weak transcription	Brain Anterior Caudate	brain

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