Variant report

Variant	rs11670239
Chromosome Location	chr19:19177481-19177482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19176303..19177932-chr19:19191338..19193529,2	K562	blood:
2	chr19:19141992..19145925-chr19:19172787..19177854,10	K562	blood:
3	chr1:76250892..76253394-chr19:19175061..19177790,2	K562	blood:
4	chr19:19174780..19176762-chr19:19177154..19178760,2	MCF-7	breast:
5	chr19:19170465..19178046-chr19:19213939..19220242,15	K562	blood:
6	chr19:19176990..19179338-chr19:19181628..19184971,3	K562	blood:
7	chr19:19141992..19145825-chr19:19171077..19177701,15	K562	blood:

Variant related genes	Relation type
ENSG00000105676	Chromatin interaction
ENSG00000206620	Chromatin interaction
ENSG00000137955	Chromatin interaction
ENSG00000064607	Chromatin interaction
ENSG00000181035	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10221504	0.98[ASN][1000 genomes]
rs10403222	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10403322	0.82[EUR][1000 genomes]
rs10404627	0.98[ASN][1000 genomes]
rs10405189	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10405635	0.98[ASN][1000 genomes]
rs10409164	0.98[ASN][1000 genomes]
rs10410451	0.98[ASN][1000 genomes]
rs10410568	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10416783	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10422335	0.85[ASN][1000 genomes]
rs10422906	0.98[ASN][1000 genomes]
rs10423742	0.98[ASN][1000 genomes]
rs10423815	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1079543	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10854005	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1124921	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11666120	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11666340	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11666627	0.98[ASN][1000 genomes]
rs11670204	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11878368	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12016	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12975676	0.98[ASN][1000 genomes]
rs12975754	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12976302	0.95[ASN][1000 genomes]
rs12978822	0.83[ASN][1000 genomes]
rs12979565	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12985799	0.98[ASN][1000 genomes]
rs1859267	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2012318	0.98[ASN][1000 genomes]
rs2107263	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2158320	0.94[ASN][1000 genomes]
rs2240094	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2240095	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2269806	0.94[ASN][1000 genomes]
rs2285851	0.94[ASN][1000 genomes]
rs2313736	0.91[ASN][1000 genomes]
rs2872394	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3180770	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4808179	0.94[ASN][1000 genomes]
rs4808184	0.98[ASN][1000 genomes]
rs4808902	0.91[ASN][1000 genomes]
rs4808904	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808905	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808906	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4808907	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808911	0.94[ASN][1000 genomes]
rs4808913	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808916	0.98[ASN][1000 genomes]
rs6511010	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6511011	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6511014	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6511015	0.94[ASN][1000 genomes]
rs6511017	0.94[ASN][1000 genomes]
rs6511018	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7248771	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7250131	0.98[ASN][1000 genomes]
rs7253244	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7255937	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7256648	0.97[ASN][1000 genomes]
rs7257635	0.94[ASN][1000 genomes]
rs7258637	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7259510	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7259609	0.98[ASN][1000 genomes]
rs8101529	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8103431	0.98[ASN][1000 genomes]
rs8104754	0.83[EUR][1000 genomes]
rs8104799	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8106146	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8107710	0.92[ASN][1000 genomes]
rs8109654	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8110629	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8111634	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8111635	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8112566	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs916898	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs929215	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9304959	0.94[ASN][1000 genomes]
rs9676917	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1059305	chr19:19131310-19209999	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
3	nsv543927	chr19:19147376-19178024	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11670239	TMEM161A	cis	Muscle Skeletal	GTEx
rs11670239	SFRS14	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19175400-19207800	Weak transcription	Aorta	Aorta
2	chr19:19176000-19184600	Weak transcription	Spleen	Spleen
3	chr19:19176200-19185800	Weak transcription	Ovary	ovary
4	chr19:19176200-19186000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr19:19176400-19177600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr19:19176400-19177600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:19176400-19177800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr19:19176400-19178000	Weak transcription	Brain Substantia Nigra	brain
9	chr19:19176400-19178200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:19176400-19178400	Enhancers	HepG2	liver
11	chr19:19176400-19178800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr19:19176400-19179400	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr19:19176400-19179800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr19:19176400-19179800	Weak transcription	Brain Germinal Matrix	brain
15	chr19:19176400-19179800	Weak transcription	Placenta	Placenta
16	chr19:19176400-19180000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:19176400-19180000	Weak transcription	Brain Anterior Caudate	brain
18	chr19:19176400-19180000	Weak transcription	Colon Smooth Muscle	Colon
19	chr19:19176400-19180000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr19:19176400-19180000	Weak transcription	Left Ventricle	heart
21	chr19:19176400-19180000	Weak transcription	Lung	lung
22	chr19:19176400-19180600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:19176400-19180600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr19:19176400-19181200	Weak transcription	Fetal Intestine Small	intestine
25	chr19:19176400-19182000	Weak transcription	Small Intestine	intestine
26	chr19:19176400-19183600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:19176400-19186200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:19176400-19189200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr19:19176400-19190400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr19:19176400-19190600	Weak transcription	Esophagus	oesophagus
31	chr19:19176400-19192600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr19:19176400-19192600	Weak transcription	Right Atrium	heart
33	chr19:19176400-19215200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr19:19176400-19215800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr19:19176400-19215800	Weak transcription	NHLF	lung
36	chr19:19176600-19177600	Weak transcription	Adipose Nuclei	Adipose
37	chr19:19176600-19177800	Enhancers	Liver	Liver
38	chr19:19176600-19177800	Weak transcription	Fetal Muscle Leg	muscle
39	chr19:19176600-19178000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:19176600-19178000	Enhancers	Primary T cells from cord blood	blood
41	chr19:19176600-19178000	Weak transcription	Brain Angular Gyrus	brain
42	chr19:19176600-19178000	Weak transcription	Brain Hippocampus Middle	brain
43	chr19:19176600-19178000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr19:19176600-19178000	Enhancers	Fetal Thymus	thymus
45	chr19:19176600-19178200	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr19:19176600-19178400	Weak transcription	HSMMtube	muscle
47	chr19:19176600-19178600	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr19:19176600-19178800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr19:19176600-19178800	Enhancers	K562	blood
50	chr19:19176600-19179600	Weak transcription	Right Ventricle	heart

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