Variant report

Variant	rs11878368
Chromosome Location	chr19:19110529-19110530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19109339..19112473-chr19:19142832..19146153,3	MCF-7	breast:
2	chr19:18880676..18881342-chr19:19110183..19110830,2	MCF-7	breast:
3	chr19:19062199..19062724-chr19:19110161..19110923,2	MCF-7	breast:
4	chr19:18557627..18558597-chr19:19110150..19110758,4	MCF-7	breast:
5	chr19:18943555..18944070-chr19:19110134..19110952,2	MCF-7	breast:
6	chr19:19110088..19110909-chr19:19169898..19170757,5	MCF-7	breast:
7	chr19:19110096..19111022-chr19:19173704..19174740,6	MCF-7	breast:
8	chr19:19110190..19110827-chr19:19162308..19163244,2	MCF-7	breast:
9	chr19:19110147..19110942-chr19:19162265..19163244,7	MCF-7	breast:
10	chr19:19109933..19111022-chr19:19173938..19174740,6	MCF-7	breast:
11	chr19:19106312..19108383-chr19:19109496..19112233,3	MCF-7	breast:
12	chr19:18557627..18558285-chr19:19110207..19110758,2	MCF-7	breast:
13	chr19:18880198..18881176-chr19:19110123..19110683,2	MCF-7	breast:
14	chr19:19062101..19062784-chr19:19110048..19110646,2	MCF-7	breast:
15	chr19:19110088..19110589-chr19:19169898..19170625,2	MCF-7	breast:
16	chr19:18943238..18944106-chr19:19110264..19111084,4	MCF-7	breast:
17	chr19:19027647..19030211-chr19:19108810..19111189,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000005007	Chromatin interaction
ENSG00000105676	Chromatin interaction
ENSG00000105669	Chromatin interaction
ENSG00000064607	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10221504	0.92[ASN][1000 genomes]
rs10403222	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10404627	0.92[ASN][1000 genomes]
rs10405189	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10405635	0.92[ASN][1000 genomes]
rs10409164	0.92[ASN][1000 genomes]
rs10410451	0.92[ASN][1000 genomes]
rs10410568	0.92[ASN][1000 genomes]
rs10416783	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10422335	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10422906	0.92[ASN][1000 genomes]
rs10423742	0.92[ASN][1000 genomes]
rs10423815	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1079543	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10854005	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1124921	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11666120	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11666340	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11666627	0.92[ASN][1000 genomes]
rs11670204	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11670239	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11671696	0.80[AMR][1000 genomes]
rs12016	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975676	0.92[ASN][1000 genomes]
rs12975754	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12976302	0.89[ASN][1000 genomes]
rs12978822	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12979565	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12985799	0.92[ASN][1000 genomes]
rs1859267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2012318	0.92[ASN][1000 genomes]
rs2107263	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2158320	0.97[ASN][1000 genomes]
rs2240094	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2240095	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2269806	0.97[ASN][1000 genomes]
rs2269869	0.85[AMR][1000 genomes]
rs2285851	0.97[ASN][1000 genomes]
rs2313736	1.00[ASN][1000 genomes]
rs2872394	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3180770	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808172	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4808179	0.97[ASN][1000 genomes]
rs4808184	0.92[ASN][1000 genomes]
rs4808902	1.00[ASN][1000 genomes]
rs4808904	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808905	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808906	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808907	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808911	0.97[ASN][1000 genomes]
rs4808913	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808916	0.92[ASN][1000 genomes]
rs6511010	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6511011	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6511014	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6511015	0.97[ASN][1000 genomes]
rs6511017	0.97[ASN][1000 genomes]
rs6511018	0.92[ASN][1000 genomes]
rs7248771	0.92[ASN][1000 genomes]
rs7249453	0.83[AFR][1000 genomes]
rs7250131	0.92[ASN][1000 genomes]
rs7253244	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7255937	0.92[ASN][1000 genomes]
rs7256648	0.91[ASN][1000 genomes]
rs7257635	0.88[ASN][1000 genomes]
rs7258637	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7259510	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7259609	0.92[ASN][1000 genomes]
rs8101529	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8103431	0.92[ASN][1000 genomes]
rs8104799	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8106146	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107710	0.87[ASN][1000 genomes]
rs8109654	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8110629	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111634	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111635	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112566	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs916898	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs929215	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9304959	0.97[ASN][1000 genomes]
rs9676917	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv2435	chr19:19077432-19122579	Strong transcription Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11878368	TMEM161A	cis	Muscle Skeletal	GTEx
rs11878368	SFRS14	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19100200-19117400	Strong transcription	Fetal Intestine Small	intestine
2	chr19:19100600-19122800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:19101000-19114000	Weak transcription	Small Intestine	intestine
4	chr19:19101000-19125600	Strong transcription	Thymus	Thymus
5	chr19:19101000-19133000	Strong transcription	Fetal Thymus	thymus
6	chr19:19101200-19126000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:19101200-19130400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr19:19101200-19140200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr19:19101400-19113000	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr19:19101400-19130400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr19:19101400-19142000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr19:19101600-19130400	Strong transcription	Primary T cells from cord blood	blood
13	chr19:19101600-19130400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr19:19102000-19113000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr19:19102000-19130200	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr19:19102000-19132000	Strong transcription	Dnd41	blood
17	chr19:19102400-19111000	Strong transcription	A549	lung
18	chr19:19102600-19122600	Weak transcription	Fetal Heart	heart
19	chr19:19103200-19130200	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr19:19103600-19123600	Strong transcription	HepG2	liver
21	chr19:19104000-19114000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr19:19105400-19110600	Weak transcription	Psoas Muscle	Psoas
23	chr19:19105600-19112000	Weak transcription	Colon Smooth Muscle	Colon
24	chr19:19105600-19112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:19106200-19112400	Weak transcription	Left Ventricle	heart
26	chr19:19106600-19112200	Weak transcription	Fetal Lung	lung
27	chr19:19106800-19112200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr19:19106800-19119200	Weak transcription	Stomach Mucosa	stomach
29	chr19:19106800-19143000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr19:19107000-19119000	Weak transcription	Fetal Kidney	kidney
31	chr19:19107200-19110800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:19107200-19130200	Strong transcription	Brain Germinal Matrix	brain
33	chr19:19107200-19142600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:19107400-19111600	Weak transcription	Fetal Brain Male	brain
35	chr19:19107400-19125800	Strong transcription	Fetal Muscle Leg	muscle
36	chr19:19107600-19127200	Strong transcription	Fetal Intestine Large	intestine
37	chr19:19107600-19130200	Strong transcription	Brain Hippocampus Middle	brain
38	chr19:19107600-19142600	Strong transcription	Fetal Stomach	stomach
39	chr19:19107800-19113000	Strong transcription	Primary B cells from cord blood	blood
40	chr19:19107800-19130200	Strong transcription	Placenta	Placenta
41	chr19:19107800-19130400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr19:19107800-19130400	Strong transcription	Fetal Brain Female	brain
43	chr19:19108000-19142000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:19108000-19142800	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr19:19108200-19111200	Strong transcription	Ovary	ovary
46	chr19:19108200-19116400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr19:19108200-19130400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:19108200-19142600	Weak transcription	Right Atrium	heart
49	chr19:19108600-19113000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr19:19108600-19119600	Strong transcription	NHDF-Ad	bronchial

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