Variant report

Variant	rs906916
Chromosome Location	chr2:191166212-191166213
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:191156936..191159599-chr2:191165960..191167883,2	MCF-7	breast:
2	chr2:191166103..191167855-chr2:191169721..191172192,2	K562	blood:
3	chr2:191164735..191167364-chr2:191183015..191185017,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198130	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12693568	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13006833	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs172366	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1876877	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2136566	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2136569	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2582735	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2582736	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2582746	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2582766	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2582770	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2664251	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2664252	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2664253	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2664259	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2664260	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs291427	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs291428	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs291429	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs291430	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs291431	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs291444	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs291445	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs291447	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs291448	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs291449	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs291453	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs291458	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs291459	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs291460	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs291461	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs291462	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs291464	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs291466	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs291468	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs291470	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs291472	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2919677	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62184386	0.87[ASN][1000 genomes]
rs6434387	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72915455	0.83[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs906916	HIBCH	cis	Thyroid	GTEx
rs906916	HIBCH	cis	Stomach	GTEx
rs906916	HIBCH	cis	lung	GTEx
rs906916	HIBCH	cis	Heart Left Ventricle	GTEx
rs906916	HIBCH	Cis_1M	lymphoblastoid	RTeQTL
rs906916	HIBCH	cis	multi-tissue	Pritchard
rs906916	HIBCH	cis	Muscle Skeletal	GTEx
rs906916	INPP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 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	chr2:191141800-191183000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:191142400-191173200	Weak transcription	NHLF	lung
14	chr2:191142600-191180200	Weak transcription	Hela-S3	cervix
15	chr2:191142600-191181200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:191143000-191167000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:191143000-191183000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:191145600-191183200	Weak transcription	HUVEC	blood vessel
19	chr2:191145800-191183000	Weak transcription	HMEC	breast
20	chr2:191146000-191171000	Weak transcription	Psoas Muscle	Psoas
21	chr2:191146000-191181200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:191146000-191181800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:191146400-191172600	Weak transcription	HSMMtube	muscle
24	chr2:191146600-191166800	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:191149000-191173400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:191149200-191176600	Weak transcription	NHEK	skin
27	chr2:191149200-191183200	Weak transcription	Fetal Kidney	kidney
28	chr2:191150800-191173200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:191150800-191173800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr2:191151000-191170800	Weak transcription	Lung	lung
31	chr2:191151000-191182800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:191151000-191183000	Weak transcription	Esophagus	oesophagus
33	chr2:191151200-191166800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:191151200-191171000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:191151400-191179200	Weak transcription	Pancreas	Pancrea
36	chr2:191151400-191179800	Weak transcription	Fetal Heart	heart
37	chr2:191151400-191180800	Weak transcription	Aorta	Aorta
38	chr2:191151400-191183000	Weak transcription	Gastric	stomach
39	chr2:191151400-191183000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:191151400-191183600	Weak transcription	Thymus	Thymus
41	chr2:191151600-191174800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr2:191152200-191171000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:191152800-191178000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:191152800-191180000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:191153400-191182800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr2:191153800-191166800	Weak transcription	Left Ventricle	heart
47	chr2:191156000-191166800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:191156200-191174200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:191156400-191167000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr2:191157600-191181400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links