Variant report

Variant	rs4129081
Chromosome Location	chr2:191307408-191307409
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	chr2:191300907..191304417-chr2:191304488..191309004,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-INPP1-1	chr2:191307302-191307731	NONHSAT076085

Variant related genes	Relation type
ENSG00000151690	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11897266	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12464923	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12472240	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12473460	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12613365	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12615925	0.86[EUR][1000 genomes]
rs12619125	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12619560	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12622496	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12693576	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12987797	0.83[EUR][1000 genomes]
rs13013848	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13019278	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13028201	0.95[CEU][hapmap];0.82[CHD][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs13029743	0.83[EUR][1000 genomes]
rs13391723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2043990	0.82[CEU][hapmap];0.81[ASN][1000 genomes]
rs34274882	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34417560	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34825614	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36055519	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3811609	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4073873	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4129697	0.82[AFR][1000 genomes]
rs4264585	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4324342	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4853508	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4853708	0.95[LWK][hapmap];0.82[AFR][1000 genomes]
rs4853709	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4853718	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4853720	0.83[EUR][1000 genomes]
rs55754136	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55987230	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6434400	0.86[EUR][1000 genomes]
rs6707773	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6707846	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6711006	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72911109	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7560318	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7564829	0.82[YRI][hapmap]
rs7601745	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7608180	0.95[CEU][hapmap];0.83[CHB][hapmap];0.83[EUR][1000 genomes]
rs9646748	0.83[ASW][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4129081	INPP1	cis	parietal	SCAN
rs4129081	HIBCH	cis	parietal	SCAN
rs4129081	HIBCH	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191284200-191311000	Weak transcription	Psoas Muscle	Psoas
2	chr2:191296800-191311400	Weak transcription	Fetal Lung	lung
3	chr2:191298600-191309000	Weak transcription	Stomach Mucosa	stomach
4	chr2:191299600-191308800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:191302000-191307800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:191302200-191308400	Weak transcription	Fetal Muscle Leg	muscle
7	chr2:191302200-191311200	Weak transcription	Fetal Stomach	stomach
8	chr2:191302200-191311400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:191302200-191319200	Weak transcription	Fetal Intestine Small	intestine
10	chr2:191302200-191321200	Weak transcription	Esophagus	oesophagus
11	chr2:191302400-191308400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr2:191302400-191331000	Weak transcription	A549	lung
13	chr2:191302600-191309000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:191302600-191309400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr2:191302600-191310600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:191302600-191311000	Weak transcription	Fetal Brain Male	brain
17	chr2:191302800-191307800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:191302800-191308600	Weak transcription	Colonic Mucosa	Colon
19	chr2:191302800-191317200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr2:191302800-191319400	Weak transcription	Fetal Brain Female	brain
21	chr2:191302800-191320200	Weak transcription	Fetal Thymus	thymus
22	chr2:191302800-191321200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:191303400-191310400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr2:191303400-191311000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:191303400-191311200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr2:191303400-191321000	Weak transcription	Thymus	Thymus
27	chr2:191303400-191321200	Weak transcription	Dnd41	blood
28	chr2:191303600-191309000	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr2:191303600-191310200	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr2:191303600-191321000	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr2:191303800-191308000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:191303800-191308400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:191303800-191321000	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr2:191303800-191331600	Weak transcription	Brain Germinal Matrix	brain
35	chr2:191303800-191332600	Weak transcription	Fetal Intestine Large	intestine
36	chr2:191304000-191308400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:191304000-191311000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:191304400-191313200	Enhancers	Brain Hippocampus Middle	brain
39	chr2:191305000-191309000	Weak transcription	Primary B cells from cord blood	blood
40	chr2:191305200-191308000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr2:191305400-191308000	Enhancers	Brain Anterior Caudate	brain
42	chr2:191305600-191308000	Enhancers	Small Intestine	intestine
43	chr2:191305600-191308600	Enhancers	Primary T cells from cord blood	blood
44	chr2:191305600-191309200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr2:191305800-191307600	Enhancers	Right Atrium	heart
46	chr2:191305800-191312000	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr2:191306000-191308600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr2:191306000-191310200	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr2:191306000-191310400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr2:191306200-191307800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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