Variant report

Variant	rs60469543
Chromosome Location	chr2:191165429-191165430
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:191164735..191167364-chr2:191183015..191185017,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198130	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1058180	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10931448	0.81[EUR][1000 genomes]
rs1114863	0.82[AMR][1000 genomes]
rs11683636	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11684995	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11685119	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11689196	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11692448	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13416673	0.81[AMR][1000 genomes]
rs1583878	0.86[AMR][1000 genomes]
rs16832420	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16832512	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs176712	0.84[AMR][1000 genomes]
rs1866850	0.80[EUR][1000 genomes]
rs2028431	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2067398	0.80[EUR][1000 genomes]
rs2067411	0.81[EUR][1000 genomes]
rs2067418	0.83[EUR][1000 genomes]
rs2067419	0.83[EUR][1000 genomes]
rs2099127	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2136567	0.83[AMR][1000 genomes]
rs2136568	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2136570	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2136571	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2256301	0.82[AMR][1000 genomes]
rs2354871	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2582738	0.84[AMR][1000 genomes]
rs2582740	0.84[AMR][1000 genomes]
rs2582742	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2582743	0.85[EUR][1000 genomes]
rs2582744	0.85[EUR][1000 genomes]
rs2582745	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2582747	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2582749	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2582753	0.81[AMR][1000 genomes]
rs2582762	0.82[AMR][1000 genomes]
rs2582763	0.82[AMR][1000 genomes]
rs2582769	0.84[AMR][1000 genomes]
rs2582771	0.83[AMR][1000 genomes]
rs2582772	0.83[AMR][1000 genomes]
rs2664241	0.84[AMR][1000 genomes]
rs2664242	0.81[AMR][1000 genomes]
rs2664244	0.83[AMR][1000 genomes]
rs2664249	0.84[AMR][1000 genomes]
rs2664255	0.84[AMR][1000 genomes]
rs2664256	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2664261	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2664266	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2664267	0.81[EUR][1000 genomes]
rs2664269	0.84[AMR][1000 genomes]
rs291411	0.88[AMR][1000 genomes]
rs291412	0.82[AMR][1000 genomes]
rs291413	0.81[AMR][1000 genomes]
rs291414	0.83[AMR][1000 genomes]
rs291419	0.83[AMR][1000 genomes]
rs291420	0.82[AMR][1000 genomes]
rs291421	0.82[AMR][1000 genomes]
rs291422	0.84[AMR][1000 genomes]
rs291424	0.83[AMR][1000 genomes]
rs291425	0.83[AMR][1000 genomes]
rs291426	0.86[AMR][1000 genomes]
rs291434	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs291435	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs291436	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs291437	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs291438	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs291439	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs291440	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs291441	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs291442	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs291446	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs291450	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs291451	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs291455	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs291463	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2919675	0.81[AMR][1000 genomes]
rs2919676	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2941092	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2966470	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35214387	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3791792	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3791800	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3791805	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3791806	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4146044	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4853684	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4853689	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4853693	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55684836	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55742982	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55815425	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56742312	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57199157	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58400804	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60068799	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61038868	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6434381	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6434382	0.87[EUR][1000 genomes]
rs66867328	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6723792	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6752703	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67791002	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72625302	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72627903	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72627904	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72627905	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7567973	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7599085	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs760307	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[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	nsv875621	chr2:191117120-191177131	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs60469543	HIBCH	Cis_1M	lymphoblastoid	RTeQTL
rs60469543	INPP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191060800-191180000	Weak transcription	Small Intestine	intestine
2	chr2:191105000-191180000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:191108200-191180000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:191115600-191182000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:191116600-191183200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:191117400-191183600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:191121000-191181400	Weak transcription	Brain Angular Gyrus	brain
8	chr2:191123200-191177600	Weak transcription	Colonic Mucosa	Colon
9	chr2:191132600-191180200	Weak transcription	NH-A	brain
10	chr2:191135600-191183200	Weak transcription	Fetal Brain Male	brain
11	chr2:191137400-191183200	Weak transcription	A549	lung
12	chr2:191140000-191165600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:191141800-191183000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:191142400-191173200	Weak transcription	NHLF	lung
15	chr2:191142600-191180200	Weak transcription	Hela-S3	cervix
16	chr2:191142600-191181200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:191143000-191167000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:191143000-191183000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:191144400-191165600	Weak transcription	Stomach Mucosa	stomach
20	chr2:191145200-191166200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:191145600-191183200	Weak transcription	HUVEC	blood vessel
22	chr2:191145800-191166000	Weak transcription	Right Ventricle	heart
23	chr2:191145800-191183000	Weak transcription	HMEC	breast
24	chr2:191146000-191171000	Weak transcription	Psoas Muscle	Psoas
25	chr2:191146000-191181200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:191146000-191181800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:191146200-191165800	Weak transcription	Brain Substantia Nigra	brain
28	chr2:191146400-191172600	Weak transcription	HSMMtube	muscle
29	chr2:191146600-191166800	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:191149000-191173400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:191149200-191176600	Weak transcription	NHEK	skin
32	chr2:191149200-191183200	Weak transcription	Fetal Kidney	kidney
33	chr2:191150800-191173200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:191150800-191173800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:191151000-191170800	Weak transcription	Lung	lung
36	chr2:191151000-191182800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:191151000-191183000	Weak transcription	Esophagus	oesophagus
38	chr2:191151200-191166800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:191151200-191171000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:191151400-191179200	Weak transcription	Pancreas	Pancrea
41	chr2:191151400-191179800	Weak transcription	Fetal Heart	heart
42	chr2:191151400-191180800	Weak transcription	Aorta	Aorta
43	chr2:191151400-191183000	Weak transcription	Gastric	stomach
44	chr2:191151400-191183000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr2:191151400-191183600	Weak transcription	Thymus	Thymus
46	chr2:191151600-191165800	Weak transcription	K562	blood
47	chr2:191151600-191174800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr2:191152200-191171000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:191152800-191178000	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr2:191152800-191180000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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