Variant report

Variant	rs2240094
Chromosome Location	chr19:19124246-19124247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19123050..19124723-chr19:19127391..19129612,2	MCF-7	breast:
2	chr19:19123249..19131135-chr19:19141063..19146907,7	K562	blood:
3	chr19:19123435..19125277-chr19:19134855..19137719,2	MCF-7	breast:
4	chr19:19123260..19126135-chr19:19127859..19130447,2	K562	blood:

Variant related genes	Relation type
ENSG00000105676	Chromatin interaction
ENSG00000064607	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1007483	1.00[JPT][hapmap]
rs10221504	0.95[ASN][1000 genomes]
rs10403222	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10404627	0.95[ASN][1000 genomes]
rs10405189	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405635	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs10409164	0.95[ASN][1000 genomes]
rs10410451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10410568	0.95[ASN][1000 genomes]
rs10414676	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10416783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417974	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10422335	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10422906	0.95[ASN][1000 genomes]
rs10423742	1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs10423815	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079543	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10854005	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1124921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666120	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11666340	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11670204	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670239	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11878368	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12975676	0.95[ASN][1000 genomes]
rs12975754	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12976302	0.92[ASN][1000 genomes]
rs12978822	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12979565	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12982014	0.80[AMR][1000 genomes]
rs12985799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1859267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2012318	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2107263	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2158320	1.00[ASN][1000 genomes]
rs2240095	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2269806	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2269869	0.91[CEU][hapmap]
rs2285851	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2313736	0.97[ASN][1000 genomes]
rs2872394	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3180770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808172	0.85[CEU][hapmap]
rs4808179	1.00[ASN][1000 genomes]
rs4808184	0.95[ASN][1000 genomes]
rs4808900	0.87[AMR][1000 genomes]
rs4808902	0.97[ASN][1000 genomes]
rs4808904	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808905	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808907	0.95[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]
rs4808911	1.00[ASN][1000 genomes]
rs4808913	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808916	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs6511010	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6511011	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6511014	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6511015	1.00[ASN][1000 genomes]
rs6511017	1.00[ASN][1000 genomes]
rs6511018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6511021	0.85[CHB][hapmap]
rs7248399	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7248771	0.95[ASN][1000 genomes]
rs7250131	0.95[ASN][1000 genomes]
rs7253244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7255937	0.95[ASN][1000 genomes]
rs7256648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7257635	0.91[ASN][1000 genomes]
rs7258637	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259510	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs757220	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs8101529	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8103431	0.95[ASN][1000 genomes]
rs8104799	0.95[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]
rs8106146	0.89[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107710	0.90[ASN][1000 genomes]
rs8109654	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110629	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111635	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8112566	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs916898	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs929215	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304959	1.00[ASN][1000 genomes]
rs9676917	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2240094	TMEM161A	cis	Muscle Skeletal	GTEx
rs2240094	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	chr19:19101000-19125600	Strong transcription	Thymus	Thymus
2	chr19:19101000-19133000	Strong transcription	Fetal Thymus	thymus
3	chr19:19101200-19126000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:19101200-19130400	Strong transcription	Duodenum Mucosa	Duodenum
5	chr19:19101200-19140200	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr19:19101400-19130400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr19:19101400-19142000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr19:19101600-19130400	Strong transcription	Primary T cells from cord blood	blood
9	chr19:19101600-19130400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:19102000-19130200	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr19:19102000-19132000	Strong transcription	Dnd41	blood
12	chr19:19103200-19130200	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr19:19106800-19143000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr19:19107200-19130200	Strong transcription	Brain Germinal Matrix	brain
15	chr19:19107200-19142600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:19107400-19125800	Strong transcription	Fetal Muscle Leg	muscle
17	chr19:19107600-19127200	Strong transcription	Fetal Intestine Large	intestine
18	chr19:19107600-19130200	Strong transcription	Brain Hippocampus Middle	brain
19	chr19:19107600-19142600	Strong transcription	Fetal Stomach	stomach
20	chr19:19107800-19130200	Strong transcription	Placenta	Placenta
21	chr19:19107800-19130400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:19107800-19130400	Strong transcription	Fetal Brain Female	brain
23	chr19:19108000-19142000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:19108000-19142800	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr19:19108200-19130400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:19108200-19142600	Weak transcription	Right Atrium	heart
27	chr19:19108600-19130600	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr19:19108600-19142200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr19:19108600-19142800	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr19:19108800-19127400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr19:19108800-19130400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr19:19109000-19130400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:19109000-19141800	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr19:19109400-19130200	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr19:19109400-19130200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr19:19109400-19142400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr19:19109800-19130200	Strong transcription	GM12878-XiMat	blood
38	chr19:19110200-19130400	Strong transcription	Stomach Smooth Muscle	stomach
39	chr19:19110600-19130000	Strong transcription	Brain Cingulate Gyrus	brain
40	chr19:19110600-19142400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr19:19111000-19126000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr19:19111000-19130200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr19:19111000-19133600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:19111200-19130200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:19111200-19130200	Strong transcription	Spleen	Spleen
46	chr19:19111200-19130400	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr19:19111200-19130400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:19111200-19130400	Strong transcription	Liver	Liver
49	chr19:19111200-19131400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:19111400-19125200	Strong transcription	Gastric	stomach

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