Variant report

Variant	rs10226865
Chromosome Location	chr7:8088394-8088395
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:8087357..8089903-chr7:8092104..8094310,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10238003	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10253861	0.88[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10264999	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10278726	1.00[CEU][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10278791	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10281919	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11981372	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1476823	0.93[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17568389	0.82[CEU][hapmap]
rs258850	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs258851	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs258852	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs37972	0.82[GIH][hapmap];0.83[TSI][hapmap]
rs37973	0.83[TSI][hapmap]
rs37974	0.83[MEX][hapmap]
rs37976	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs37979	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs37982	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs37986	1.00[CEU][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs37987	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs37996	0.83[AFR][1000 genomes]
rs37997	0.85[CEU][hapmap]
rs38000	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38007	0.84[CEU][hapmap];0.81[AFR][1000 genomes]
rs38008	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs38009	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs38015	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4256496	1.00[CEU][hapmap]
rs4725055	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4725056	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4725059	0.85[CEU][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6463753	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6463758	0.84[YRI][hapmap];0.84[AMR][1000 genomes]
rs6953808	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7796831	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7808399	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7810540	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9655516	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10226865	GLCCI1	cis	parietal	SCAN
rs10226865	LOC389458	cis	cerebellum	SCAN
rs10226865	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8041600-8095000	Weak transcription	Gastric	stomach
2	chr7:8043000-8099200	Weak transcription	Colon Smooth Muscle	Colon
3	chr7:8047600-8108200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr7:8064400-8096200	Weak transcription	NHLF	lung
5	chr7:8065000-8095000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:8065000-8108600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:8066400-8090800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr7:8066400-8096600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr7:8066400-8127600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:8066600-8099800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr7:8066600-8126000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr7:8066800-8091200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr7:8066800-8095000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr7:8066800-8095600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr7:8066800-8099800	Weak transcription	Brain Anterior Caudate	brain
16	chr7:8066800-8108600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr7:8067000-8091800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr7:8067000-8135400	Weak transcription	Pancreas	Pancrea
19	chr7:8067200-8095600	Weak transcription	Fetal Lung	lung
20	chr7:8067600-8095800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:8068000-8095600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:8069800-8095800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:8075000-8108600	Weak transcription	Psoas Muscle	Psoas
24	chr7:8075000-8125800	Weak transcription	Lung	lung
25	chr7:8075000-8126800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:8075600-8095000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr7:8075600-8095000	Weak transcription	Aorta	Aorta
28	chr7:8075600-8095000	Weak transcription	Ovary	ovary
29	chr7:8075600-8095200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:8075600-8101400	Weak transcription	K562	blood
31	chr7:8075600-8104400	Weak transcription	HMEC	breast
32	chr7:8075600-8105000	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr7:8075600-8113000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr7:8075600-8131800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr7:8075800-8095200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr7:8075800-8095400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr7:8076000-8088800	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr7:8076000-8095000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr7:8076000-8095000	Weak transcription	Fetal Intestine Large	intestine
40	chr7:8076000-8111800	Weak transcription	Fetal Brain Male	brain
41	chr7:8076000-8124200	Weak transcription	Fetal Kidney	kidney
42	chr7:8076200-8102200	Weak transcription	Fetal Brain Female	brain
43	chr7:8076200-8108400	Weak transcription	Brain Angular Gyrus	brain
44	chr7:8076800-8088800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr7:8076800-8095600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr7:8077000-8095000	Weak transcription	Adipose Nuclei	Adipose
47	chr7:8077000-8095000	Weak transcription	Fetal Muscle Leg	muscle
48	chr7:8077200-8089600	Weak transcription	Brain Germinal Matrix	brain
49	chr7:8077200-8095000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr7:8077200-8095000	Weak transcription	Brain Hippocampus Middle	brain

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