Variant report

Variant	rs11544940
Chromosome Location	chr2:191231458-191231459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFATC1	chr2:191230347-191231470	GM12878	blood:	n/a	n/a
2	BCL3	chr2:191230313-191231529	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:191229901..191232788-chr2:191235811..191237515,2	MCF-7	breast:
2	chr2:191229465..191231914-chr2:191232411..191236009,3	K562	blood:

Variant related genes	Relation type
INPP1	TF binding region
ENSG00000151689	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12471159	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693568	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1530225	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1530226	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984626	0.81[YRI][hapmap]
rs2006980	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067416	0.81[YRI][hapmap]
rs2067434	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2067446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2582736	1.00[JPT][hapmap]
rs291430	0.83[ASN][1000 genomes]
rs291445	1.00[JPT][hapmap]
rs291447	1.00[JPT][hapmap]
rs291449	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs291458	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs291460	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs291468	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs35277625	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3791809	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs56044907	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6434387	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6730620	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590991	0.92[CEU][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap]
rs909270	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs909272	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9784054	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11544940	MFSD6	cis	cerebellum	SCAN
rs11544940	HIBCH	cis	parietal	SCAN
rs11544940	INPP1	cis	lymphoblastoid	seeQTL
rs11544940	HIBCH	cis	Muscle Skeletal	GTEx
rs11544940	HIBCH	cis	multi-tissue	Pritchard
rs11544940	INPP1	cis	cerebellum	SCAN
rs11544940	INPP1	cis	parietal	SCAN
rs11544940	HIBCH	cis	lymphoblastoid	seeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191211400-191238000	Weak transcription	Hela-S3	cervix
2	chr2:191219400-191234000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:191219600-191243800	Weak transcription	Gastric	stomach
4	chr2:191223800-191236800	Weak transcription	Psoas Muscle	Psoas
5	chr2:191224000-191235600	Weak transcription	Spleen	Spleen
6	chr2:191224800-191236200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr2:191225000-191232000	Weak transcription	Ovary	ovary
8	chr2:191225000-191232800	Weak transcription	HUVEC	blood vessel
9	chr2:191225000-191234200	Weak transcription	Right Ventricle	heart
10	chr2:191225000-191235600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:191225000-191235600	Weak transcription	Pancreas	Pancrea
12	chr2:191225000-191236400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr2:191225000-191237400	Weak transcription	Fetal Brain Female	brain
14	chr2:191225000-191237600	Weak transcription	Small Intestine	intestine
15	chr2:191225000-191242800	Weak transcription	Placenta	Placenta
16	chr2:191225200-191231800	Weak transcription	HSMMtube	muscle
17	chr2:191225200-191232000	Weak transcription	HepG2	liver
18	chr2:191225200-191232000	Weak transcription	Osteobl	bone
19	chr2:191225200-191233000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:191225200-191233400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:191225200-191233800	Weak transcription	NHLF	lung
22	chr2:191225200-191234400	Weak transcription	K562	blood
23	chr2:191225200-191235200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:191225200-191235200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:191225200-191235600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:191225200-191235600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:191225200-191235600	Weak transcription	Colonic Mucosa	Colon
28	chr2:191225200-191235800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:191225200-191235800	Weak transcription	Brain Germinal Matrix	brain
30	chr2:191225200-191236200	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr2:191225200-191236400	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:191225200-191236600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:191225200-191236600	Weak transcription	NH-A	brain
34	chr2:191225200-191237000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:191225200-191237000	Weak transcription	Stomach Mucosa	stomach
36	chr2:191225200-191237000	Weak transcription	HMEC	breast
37	chr2:191225200-191237200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:191225200-191237200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr2:191225200-191238200	Weak transcription	NHEK	skin
40	chr2:191225200-191242800	Weak transcription	Fetal Kidney	kidney
41	chr2:191225200-191244000	Weak transcription	Fetal Heart	heart
42	chr2:191225200-191244800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr2:191225400-191232200	Weak transcription	Primary B cells from cord blood	blood
44	chr2:191225400-191236200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:191225400-191237200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:191225400-191239200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr2:191225600-191232400	Weak transcription	NHDF-Ad	bronchial
48	chr2:191225800-191234000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:191226000-191232400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr2:191226000-191232800	Weak transcription	HSMM	muscle

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