Variant report

Variant	rs10197348
Chromosome Location	chr2:191300118-191300119
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	SPI1	chr2:191300065-191300295	GM12878	blood:	n/a	chr2:191300212-191300225 chr2:191300214-191300221 chr2:191300213-191300222
2	SPI1	chr2:191300057-191300317	GM12891	blood:	n/a	chr2:191300212-191300225 chr2:191300214-191300221 chr2:191300213-191300222
3	SPI1	chr2:191300063-191300474	HL-60	blood:	n/a	chr2:191300212-191300225 chr2:191300214-191300221 chr2:191300213-191300222
4	RUNX3	chr2:191300003-191300415	GM12878	blood:	n/a	chr2:191300233-191300242
5	SPI1	chr2:191299944-191300509	HL-60	blood:	n/a	chr2:191300212-191300225 chr2:191300214-191300221 chr2:191300213-191300222
6	SPI1	chr2:191300081-191300326	GM12891	blood:	n/a	chr2:191300212-191300225 chr2:191300214-191300221 chr2:191300213-191300222

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:191272728..191274553-chr2:191298568..191301564,2	MCF-7	breast:

Variant related genes	Relation type
MFSD6	TF binding region
ENSG00000151690	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10084203	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10174174	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10188341	0.85[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10190082	0.80[CEU][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10931451	0.88[ASN][1000 genomes]
rs10931458	0.81[CEU][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1128723	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs12052514	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs12053190	0.95[JPT][hapmap]
rs12172905	0.88[ASN][1000 genomes]
rs12472081	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs13417431	0.95[ASN][1000 genomes]
rs16832765	0.85[JPT][hapmap]
rs1866851	0.88[ASN][1000 genomes]
rs2043990	0.82[YRI][hapmap]
rs4129082	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4258824	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs4261750	0.92[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4287794	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4340549	0.83[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4439990	0.95[JPT][hapmap]
rs4641969	0.81[CEU][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4853510	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4853710	0.95[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4853716	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56127319	0.93[ASN][1000 genomes]
rs56342910	0.89[ASN][1000 genomes]
rs59929070	0.91[ASN][1000 genomes]
rs61709084	0.95[ASN][1000 genomes]
rs62180987	0.88[ASN][1000 genomes]
rs62180990	0.85[ASN][1000 genomes]
rs62180992	0.95[ASN][1000 genomes]
rs62181018	0.91[ASN][1000 genomes]
rs62181019	0.91[ASN][1000 genomes]
rs62181020	0.91[ASN][1000 genomes]
rs6712426	0.80[AMR][1000 genomes]
rs6731287	0.95[JPT][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7569128	0.85[JPT][hapmap]
rs7581762	0.95[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7581986	0.85[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7593240	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10197348	MFSD6	cis	cerebellum	SCAN
rs10197348	INPP1	cis	cerebellum	SCAN
rs10197348	ITPRIP	trans	cerebellum	SCAN
rs10197348	INPP1	cis	parietal	SCAN
rs10197348	MSTN	cis	cerebellum	SCAN
rs10197348	INPP1	Cis_1M	lymphoblastoid	RTeQTL
rs10197348	HIBCH	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191273800-191301400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:191274800-191300800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:191278600-191301200	Weak transcription	Pancreas	Pancrea
4	chr2:191278800-191300800	Weak transcription	Fetal Thymus	thymus
5	chr2:191278800-191301200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:191279000-191300800	Weak transcription	Esophagus	oesophagus
7	chr2:191279200-191303000	Weak transcription	NHEK	skin
8	chr2:191282800-191301200	Weak transcription	Fetal Brain Male	brain
9	chr2:191283200-191301000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:191284200-191301000	Weak transcription	Gastric	stomach
11	chr2:191284200-191301200	Weak transcription	Right Ventricle	heart
12	chr2:191284200-191311000	Weak transcription	Psoas Muscle	Psoas
13	chr2:191285600-191301000	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:191287000-191300800	Weak transcription	Brain Germinal Matrix	brain
15	chr2:191290400-191301200	Weak transcription	Brain Anterior Caudate	brain
16	chr2:191290800-191300800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:191292200-191300800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:191292200-191301000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:191293200-191301000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:191293200-191301200	Weak transcription	Brain Substantia Nigra	brain
21	chr2:191293200-191301600	Weak transcription	A549	lung
22	chr2:191293400-191300600	Weak transcription	Dnd41	blood
23	chr2:191296400-191300200	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr2:191296400-191300400	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr2:191296400-191300400	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr2:191296400-191300800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:191296600-191300800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:191296800-191300400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:191296800-191300600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:191296800-191311400	Weak transcription	Fetal Lung	lung
31	chr2:191297000-191301200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:191297000-191301200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:191297000-191301600	Weak transcription	Fetal Intestine Small	intestine
34	chr2:191297200-191300800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:191297200-191300800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:191297200-191300800	Weak transcription	Colonic Mucosa	Colon
37	chr2:191297200-191300800	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:191297200-191300800	Weak transcription	Thymus	Thymus
39	chr2:191297200-191301000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:191297200-191301200	Weak transcription	Adipose Nuclei	Adipose
41	chr2:191297200-191301200	Weak transcription	Fetal Stomach	stomach
42	chr2:191297200-191301200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr2:191297200-191306200	Weak transcription	K562	blood
44	chr2:191297400-191300800	Weak transcription	Aorta	Aorta
45	chr2:191297400-191300800	Weak transcription	Fetal Intestine Large	intestine
46	chr2:191297400-191300800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr2:191297400-191301000	Weak transcription	Left Ventricle	heart
48	chr2:191297400-191301200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr2:191297400-191301200	Weak transcription	Ovary	ovary
50	chr2:191297400-191301200	Weak transcription	Spleen	Spleen

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