Variant report

Variant	rs4725059
Chromosome Location	chr7:8077779-8077780
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10226865	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]
rs10238003	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10264999	0.85[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10278726	0.85[CEU][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10278791	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10281919	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11981372	0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476823	0.85[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs258850	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs258851	0.85[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs258852	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs37976	0.85[CEU][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs37979	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs37982	0.85[EUR][1000 genomes]
rs37986	0.85[CEU][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs37987	0.85[CEU][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs37996	0.84[AFR][1000 genomes]
rs38000	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs38007	0.80[AFR][1000 genomes]
rs38008	0.85[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38009	0.85[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs38015	0.85[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4256496	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs4725055	0.84[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4725056	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6463753	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6953808	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7796831	0.84[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7808399	0.85[CEU][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7810540	0.85[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9655516	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv1793794	chr7:8064509-8078802	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4725059	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 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	chr7:8066600-8082000	Weak transcription	Osteobl	bone
11	chr7:8066600-8099800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr7:8066600-8126000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr7:8066800-8082600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr7:8066800-8091200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr7:8066800-8095000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:8066800-8095600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr7:8066800-8099800	Weak transcription	Brain Anterior Caudate	brain
18	chr7:8066800-8108600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr7:8067000-8078400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr7:8067000-8091800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr7:8067000-8135400	Weak transcription	Pancreas	Pancrea
22	chr7:8067200-8084000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:8067200-8095600	Weak transcription	Fetal Lung	lung
24	chr7:8067400-8082800	Weak transcription	Hela-S3	cervix
25	chr7:8067600-8095800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr7:8068000-8095600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr7:8069800-8095800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr7:8074200-8078400	Strong transcription	Dnd41	blood
29	chr7:8074200-8078600	ZNF genes & repeats	GM12878-XiMat	blood
30	chr7:8075000-8108600	Weak transcription	Psoas Muscle	Psoas
31	chr7:8075000-8125800	Weak transcription	Lung	lung
32	chr7:8075000-8126800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr7:8075200-8078600	Strong transcription	Primary B cells from cord blood	blood
34	chr7:8075400-8078600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr7:8075600-8078600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr7:8075600-8080000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr7:8075600-8080000	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr7:8075600-8082400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr7:8075600-8083800	Weak transcription	Fetal Stomach	stomach
40	chr7:8075600-8095000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr7:8075600-8095000	Weak transcription	Aorta	Aorta
42	chr7:8075600-8095000	Weak transcription	Ovary	ovary
43	chr7:8075600-8095200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:8075600-8101400	Weak transcription	K562	blood
45	chr7:8075600-8104400	Weak transcription	HMEC	breast
46	chr7:8075600-8105000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr7:8075600-8113000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:8075600-8131800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr7:8075800-8078400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr7:8075800-8079800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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