Variant report

Variant	rs11666120
Chromosome Location	chr19:19131900-19131901
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19131657..19133627-chr19:19143750..19145412,2	K562	blood:
2	chr19:19131657..19140875-chr19:19141068..19145619,15	K562	blood:
3	chr19:19129913..19132824-chr19:19171752..19174736,2	K562	blood:

Variant related genes	Relation type
ENSG00000105676	Chromatin interaction
ENSG00000064607	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10221504	0.94[ASN][1000 genomes]
rs10403222	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10404627	0.94[ASN][1000 genomes]
rs10405189	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10405635	0.94[ASN][1000 genomes]
rs10409164	0.94[ASN][1000 genomes]
rs10410451	0.94[ASN][1000 genomes]
rs10410568	0.94[ASN][1000 genomes]
rs10416783	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10422335	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10422906	0.94[ASN][1000 genomes]
rs10423742	0.94[ASN][1000 genomes]
rs10423815	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1079543	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10854005	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1124921	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11666340	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11666627	0.94[ASN][1000 genomes]
rs11670204	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11670239	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11878368	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12016	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12975676	0.94[ASN][1000 genomes]
rs12975754	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12976302	0.91[ASN][1000 genomes]
rs12978822	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12979565	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12982014	0.80[AMR][1000 genomes]
rs12985799	0.94[ASN][1000 genomes]
rs1859267	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2012318	0.94[ASN][1000 genomes]
rs2107263	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2158320	0.98[ASN][1000 genomes]
rs2240094	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240095	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2269806	0.98[ASN][1000 genomes]
rs2285851	0.98[ASN][1000 genomes]
rs2313736	0.95[ASN][1000 genomes]
rs2872394	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3180770	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808179	0.98[ASN][1000 genomes]
rs4808184	0.94[ASN][1000 genomes]
rs4808900	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4808902	0.95[ASN][1000 genomes]
rs4808904	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808905	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808906	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808907	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808911	0.98[ASN][1000 genomes]
rs4808913	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808916	0.94[ASN][1000 genomes]
rs6511010	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511011	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6511014	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511015	0.98[ASN][1000 genomes]
rs6511017	0.98[ASN][1000 genomes]
rs6511018	0.94[ASN][1000 genomes]
rs7248771	0.94[ASN][1000 genomes]
rs7250131	0.94[ASN][1000 genomes]
rs7253244	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7255937	0.94[ASN][1000 genomes]
rs7256648	0.92[ASN][1000 genomes]
rs7257635	0.90[ASN][1000 genomes]
rs7258637	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7259510	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7259609	0.94[ASN][1000 genomes]
rs8101529	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8103431	0.94[ASN][1000 genomes]
rs8104799	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8106146	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8107710	0.88[ASN][1000 genomes]
rs8109654	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8110629	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8111634	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8111635	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8112566	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs916898	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs929215	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9304959	0.98[ASN][1000 genomes]
rs9676917	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11666120	TMEM161A	cis	Muscle Skeletal	GTEx
rs11666120	SFRS14	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19101000-19133000	Strong transcription	Fetal Thymus	thymus
2	chr19:19101200-19140200	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr19:19101400-19142000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr19:19102000-19132000	Strong transcription	Dnd41	blood
5	chr19:19106800-19143000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:19107200-19142600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:19107600-19142600	Strong transcription	Fetal Stomach	stomach
8	chr19:19108000-19142000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:19108000-19142800	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr19:19108200-19142600	Weak transcription	Right Atrium	heart
11	chr19:19108600-19142200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr19:19108600-19142800	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:19109000-19141800	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr19:19109400-19142400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:19110600-19142400	Strong transcription	Fetal Muscle Trunk	muscle
16	chr19:19111000-19133600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:19123600-19133600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr19:19124000-19133400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:19124600-19133200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr19:19126400-19143400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr19:19126600-19137600	Strong transcription	Fetal Muscle Leg	muscle
22	chr19:19126800-19142600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:19127000-19133200	Strong transcription	Thymus	Thymus
24	chr19:19127800-19133200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr19:19127800-19135200	Weak transcription	Psoas Muscle	Psoas
26	chr19:19128000-19142200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:19128000-19142800	Strong transcription	Fetal Intestine Small	intestine
28	chr19:19128000-19142800	Weak transcription	Stomach Mucosa	stomach
29	chr19:19128200-19132200	Weak transcription	Colon Smooth Muscle	Colon
30	chr19:19128400-19136200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr19:19129800-19133200	Weak transcription	Fetal Brain Male	brain
32	chr19:19130000-19132000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr19:19130000-19132000	Weak transcription	NHDF-Ad	bronchial
34	chr19:19130000-19132200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr19:19130000-19132600	Weak transcription	Pancreas	Pancrea
36	chr19:19130200-19132000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr19:19130200-19132000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr19:19130200-19132000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr19:19130200-19132000	Weak transcription	Brain Angular Gyrus	brain
40	chr19:19130200-19132000	Weak transcription	Brain Anterior Caudate	brain
41	chr19:19130200-19132000	Weak transcription	Brain Hippocampus Middle	brain
42	chr19:19130200-19132000	Weak transcription	Brain Substantia Nigra	brain
43	chr19:19130200-19132000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr19:19130200-19132000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr19:19130200-19132000	Weak transcription	Spleen	Spleen
46	chr19:19130200-19132000	Weak transcription	A549	lung
47	chr19:19130200-19132000	Weak transcription	GM12878-XiMat	blood
48	chr19:19130200-19132000	Weak transcription	HSMMtube	muscle
49	chr19:19130200-19132000	Weak transcription	HUVEC	blood vessel
50	chr19:19130200-19132000	Weak transcription	NH-A	brain

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