Variant report

Variant	rs1966477
Chromosome Location	chr5:112172786-112172787
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112172653..112174509-chr5:112195056..112196675,2	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10463643	0.81[EUR][1000 genomes]
rs1093677	0.81[ASN][1000 genomes]
rs12656359	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1441375	0.85[EUR][1000 genomes]
rs151976	0.81[ASN][1000 genomes]
rs151977	0.81[ASN][1000 genomes]
rs151978	0.81[ASN][1000 genomes]
rs153545	0.81[ASN][1000 genomes]
rs1661035	0.87[EUR][1000 genomes]
rs1661036	0.86[EUR][1000 genomes]
rs1734243	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs187075	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1966476	0.87[EUR][1000 genomes]
rs2229992	0.85[EUR][1000 genomes]
rs2431240	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2439591	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2464805	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2545159	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2545162	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2545163	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2545164	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2545165	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2545166	0.83[ASN][1000 genomes]
rs2545167	0.83[ASN][1000 genomes]
rs2545169	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2546110	0.85[EUR][1000 genomes]
rs2546111	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2546116	0.87[EUR][1000 genomes]
rs2909786	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2909787	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2909904	0.83[ASN][1000 genomes]
rs2909958	0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2952615	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs351769	0.82[ASN][1000 genomes]
rs351771	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35726351	0.81[ASN][1000 genomes]
rs372492	0.83[ASN][1000 genomes]
rs382260	0.83[ASN][1000 genomes]
rs386830	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs392907	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs395266	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs397768	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs401908	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41115	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs411356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419632	0.81[ASN][1000 genomes]
rs42427	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs429427	0.82[ASN][1000 genomes]
rs430665	0.81[ASN][1000 genomes]
rs431287	0.83[ASN][1000 genomes]
rs433429	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs434090	0.81[ASN][1000 genomes]
rs439456	0.83[ASN][1000 genomes]
rs455469	0.81[ASN][1000 genomes]
rs458967	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs460301	0.82[ASN][1000 genomes]
rs460832	0.81[ASN][1000 genomes]
rs461866	0.81[ASN][1000 genomes]
rs463229	0.82[ASN][1000 genomes]
rs464002	0.91[EUR][1000 genomes]
rs464708	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs465454	0.81[ASN][1000 genomes]
rs465899	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs468179	0.87[EUR][1000 genomes]
rs469663	0.81[ASN][1000 genomes]
rs481789	0.84[ASN][1000 genomes]
rs497844	0.88[ASN][1000 genomes]
rs501250	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs519397	0.81[ASN][1000 genomes]
rs529076	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs563556	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs565453	0.86[ASN][1000 genomes]
rs565603	0.88[ASN][1000 genomes]
rs569940	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs580237	0.83[ASN][1000 genomes]
rs712662	0.80[ASN][1000 genomes]
rs712664	0.81[ASN][1000 genomes]
rs712665	0.81[ASN][1000 genomes]
rs712668	0.83[ASN][1000 genomes]
rs712671	0.83[ASN][1000 genomes]
rs818423	0.81[ASN][1000 genomes]
rs864682	0.81[ASN][1000 genomes]
rs866006	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9011	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032464	chr5:112076061-112192380	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	nsv537862	chr5:112076061-112192380	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv1034239	chr5:112161239-112194693	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1966477	SRP19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112093400-112183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:112103000-112173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:112118200-112177000	Weak transcription	Colonic Mucosa	Colon
4	chr5:112132000-112174000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:112132800-112179800	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:112136600-112176200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr5:112140400-112183800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:112149400-112176400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr5:112150200-112177800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:112151400-112176400	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr5:112152000-112183800	Weak transcription	Gastric	stomach
12	chr5:112153200-112179400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:112153200-112179800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:112154000-112175200	Weak transcription	Stomach Mucosa	stomach
15	chr5:112154400-112179400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr5:112154600-112177800	Strong transcription	Primary T cells from cord blood	blood
17	chr5:112155000-112183800	Weak transcription	Aorta	Aorta
18	chr5:112155200-112173600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:112155800-112173400	Weak transcription	Pancreas	Pancrea
20	chr5:112155800-112173800	Weak transcription	Hela-S3	cervix
21	chr5:112156000-112173400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:112156000-112173400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr5:112156000-112173400	Weak transcription	Fetal Heart	heart
24	chr5:112156200-112179000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:112158600-112173200	Weak transcription	Fetal Kidney	kidney
26	chr5:112158800-112173400	Weak transcription	Fetal Brain Male	brain
27	chr5:112160600-112176200	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr5:112162000-112172800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr5:112162000-112175200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr5:112162600-112174600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:112163400-112183800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr5:112164000-112175200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr5:112164200-112173200	Weak transcription	NHEK	skin
34	chr5:112164200-112173400	Weak transcription	HUVEC	blood vessel
35	chr5:112164400-112173400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr5:112164600-112173200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr5:112165000-112172800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr5:112165200-112173400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr5:112165400-112173200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr5:112165400-112173200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:112165400-112182400	Weak transcription	Right Ventricle	heart
42	chr5:112165600-112173000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr5:112165600-112173200	Weak transcription	Esophagus	oesophagus
44	chr5:112165600-112173400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:112165600-112173400	Weak transcription	Ovary	ovary
46	chr5:112165600-112173400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr5:112165600-112173400	Weak transcription	Spleen	Spleen
48	chr5:112165600-112174000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr5:112165800-112173200	Weak transcription	Psoas Muscle	Psoas
50	chr5:112165800-112173400	Weak transcription	Small Intestine	intestine

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