Variant report

Variant	rs291447
Chromosome Location	chr2:191177005-191177006
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	chr2:191176802..191182284-chr2:191182793..191185787,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198130	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11544940	1.00[JPT][hapmap]
rs12471159	1.00[JPT][hapmap]
rs12693568	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13006833	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1530226	1.00[JPT][hapmap]
rs172366	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1866849	0.85[YRI][hapmap]
rs1876877	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2067434	1.00[JPT][hapmap]
rs2067446	1.00[JPT][hapmap]
rs2136566	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2136569	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2256301	0.82[YRI][hapmap]
rs2582735	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2582736	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2582743	0.84[YRI][hapmap]
rs2582744	0.81[YRI][hapmap]
rs2582746	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2582766	0.86[EUR][1000 genomes]
rs2582770	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2664251	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2664252	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2664253	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2664256	0.83[YRI][hapmap]
rs2664259	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2664260	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs291413	0.82[YRI][hapmap]
rs291418	0.84[YRI][hapmap]
rs291427	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs291428	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs291429	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs291430	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs291431	1.00[CEU][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs291435	0.89[YRI][hapmap]
rs291444	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs291445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs291448	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs291449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs291451	0.88[YRI][hapmap]
rs291453	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs291458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs291459	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs291460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs291461	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs291462	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs291463	0.86[YRI][hapmap]
rs291464	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs291466	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs291468	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs291470	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs291472	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2919677	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3791800	0.84[YRI][hapmap]
rs3791809	1.00[JPT][hapmap]
rs6434387	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7590991	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs906916	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs909270	1.00[JPT][hapmap]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs291447	HIBCH	cis	Thyroid	GTEx
rs291447	HIBCH	cis	Muscle Skeletal	GTEx
rs291447	HIBCH	cis	Stomach	GTEx
rs291447	HIBCH	cis	Heart Left Ventricle	GTEx
rs291447	HIBCH	cis	Lymphoblastoid	GTEx
rs291447	HIBCH	cis	multi-tissue	Pritchard
rs291447	HIBCH	cis	lung	GTEx
rs291447	HIBCH	Cis_1M	lymphoblastoid	RTeQTL
rs291447	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	chr2:191141800-191183000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:191142600-191180200	Weak transcription	Hela-S3	cervix
14	chr2:191142600-191181200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:191143000-191183000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:191145600-191183200	Weak transcription	HUVEC	blood vessel
17	chr2:191145800-191183000	Weak transcription	HMEC	breast
18	chr2:191146000-191181200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:191146000-191181800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:191149200-191183200	Weak transcription	Fetal Kidney	kidney
21	chr2:191151000-191182800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:191151000-191183000	Weak transcription	Esophagus	oesophagus
23	chr2:191151400-191179200	Weak transcription	Pancreas	Pancrea
24	chr2:191151400-191179800	Weak transcription	Fetal Heart	heart
25	chr2:191151400-191180800	Weak transcription	Aorta	Aorta
26	chr2:191151400-191183000	Weak transcription	Gastric	stomach
27	chr2:191151400-191183000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:191151400-191183600	Weak transcription	Thymus	Thymus
29	chr2:191152800-191178000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:191152800-191180000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:191153400-191182800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr2:191157600-191181400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:191160400-191180000	Weak transcription	Osteobl	bone
34	chr2:191160400-191181400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr2:191160600-191180000	Weak transcription	NHDF-Ad	bronchial
36	chr2:191161200-191181400	Weak transcription	Spleen	Spleen
37	chr2:191161400-191183600	Weak transcription	Ovary	ovary
38	chr2:191161800-191180000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:191162200-191182200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:191165000-191179800	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:191165400-191183000	Weak transcription	Fetal Brain Female	brain
42	chr2:191166200-191183200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr2:191166600-191182800	Weak transcription	Right Atrium	heart
44	chr2:191167000-191183000	Weak transcription	Brain Germinal Matrix	brain
45	chr2:191167200-191179800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:191167200-191182800	Weak transcription	Right Ventricle	heart
47	chr2:191167400-191178600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:191167400-191180000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr2:191167600-191183200	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr2:191168000-191183000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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