Variant report

Variant	rs2269869
Chromosome Location	chr19:19109545-19109546
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19109339..19112473-chr19:19142832..19146153,3	MCF-7	breast:
2	chr19:19106780..19109822-chr19:19115561..19117365,3	MCF-7	breast:
3	chr19:19108789..19110296-chr19:19117507..19119066,2	K562	blood:
4	chr19:19106312..19108383-chr19:19109496..19112233,3	MCF-7	breast:
5	chr19:19027647..19030211-chr19:19108810..19111189,2	MCF-7	breast:

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

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10403272	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10416783	0.91[CEU][hapmap]
rs10422335	0.81[AMR][1000 genomes]
rs1079543	0.90[CEU][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10854005	0.84[CEU][hapmap]
rs11085249	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11666340	0.84[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11670204	0.85[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs11671696	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878368	0.85[AMR][1000 genomes]
rs12016	0.91[CEU][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12975754	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12979565	0.84[CEU][hapmap]
rs1859267	0.89[CEU][hapmap];0.85[AMR][1000 genomes]
rs2013813	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2240094	0.91[CEU][hapmap]
rs2240095	0.91[AFR][1000 genomes]
rs2872394	0.84[CEU][hapmap]
rs3180770	0.90[CEU][hapmap];0.82[AMR][1000 genomes]
rs3787041	0.85[JPT][hapmap]
rs4808172	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808176	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4808895	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4808900	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808904	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4808905	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs4808906	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs4808907	0.84[CEU][hapmap]
rs4808913	0.84[CEU][hapmap]
rs4808916	0.85[JPT][hapmap]
rs4808917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6511010	0.84[CEU][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes]
rs7249453	0.97[YRI][hapmap]
rs7252615	0.91[ASN][1000 genomes]
rs7253244	0.90[CEU][hapmap]
rs7259510	0.83[AMR][1000 genomes]
rs8104799	0.84[CEU][hapmap]
rs8110629	0.84[CEU][hapmap]
rs8111634	0.90[CEU][hapmap]
rs8111635	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs929215	0.84[CEU][hapmap];0.86[YRI][hapmap]
rs9676917	0.93[AFR][1000 genomes];0.83[AMR][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
rs2269869	TMEM161A	cis	Muscle Skeletal	GTEx
rs2269869	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	chr19:19098600-19109800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr19:19100200-19117400	Strong transcription	Fetal Intestine Small	intestine
3	chr19:19100600-19122800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:19101000-19109800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:19101000-19114000	Weak transcription	Small Intestine	intestine
6	chr19:19101000-19125600	Strong transcription	Thymus	Thymus
7	chr19:19101000-19133000	Strong transcription	Fetal Thymus	thymus
8	chr19:19101200-19109800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr19:19101200-19109800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr19:19101200-19110400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr19:19101200-19126000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr19:19101200-19130400	Strong transcription	Duodenum Mucosa	Duodenum
13	chr19:19101200-19140200	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr19:19101400-19109800	Strong transcription	Liver	Liver
15	chr19:19101400-19113000	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr19:19101400-19130400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr19:19101400-19142000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr19:19101600-19130400	Strong transcription	Primary T cells from cord blood	blood
19	chr19:19101600-19130400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:19101800-19109600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:19101800-19109600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr19:19101800-19109600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:19102000-19110000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr19:19102000-19113000	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr19:19102000-19130200	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr19:19102000-19132000	Strong transcription	Dnd41	blood
27	chr19:19102200-19110400	Strong transcription	Gastric	stomach
28	chr19:19102400-19109800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr19:19102400-19111000	Strong transcription	A549	lung
30	chr19:19102600-19122600	Weak transcription	Fetal Heart	heart
31	chr19:19103200-19130200	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr19:19103600-19109600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr19:19103600-19123600	Strong transcription	HepG2	liver
34	chr19:19104000-19114000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr19:19105000-19109800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr19:19105200-19110000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:19105400-19110600	Weak transcription	Psoas Muscle	Psoas
38	chr19:19105600-19109800	Weak transcription	K562	blood
39	chr19:19105600-19112000	Weak transcription	Colon Smooth Muscle	Colon
40	chr19:19105600-19112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:19105800-19110200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr19:19106000-19110000	Weak transcription	HSMM	muscle
43	chr19:19106200-19112400	Weak transcription	Left Ventricle	heart
44	chr19:19106600-19109800	Weak transcription	HSMMtube	muscle
45	chr19:19106600-19110000	Weak transcription	Hela-S3	cervix
46	chr19:19106600-19112200	Weak transcription	Fetal Lung	lung
47	chr19:19106800-19109800	Weak transcription	GM12878-XiMat	blood
48	chr19:19106800-19110000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr19:19106800-19112200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr19:19106800-19119200	Weak transcription	Stomach Mucosa	stomach

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