Variant report

Variant	rs4725060
Chromosome Location	chr7:8077913-8077914
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10215645	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10226050	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10228900	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10229643	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10231036	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10241457	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10243846	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10246564	0.82[CEU][hapmap]
rs10247928	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10248588	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10258788	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10273241	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10486205	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11976862	0.82[YRI][hapmap]
rs11984078	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12702692	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12702693	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17568389	0.90[CHB][hapmap];0.92[JPT][hapmap];0.97[YRI][hapmap];0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2079853	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2109382	0.93[CEU][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2191321	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2348774	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs258853	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28488572	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28670736	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3735457	0.82[CEU][hapmap];0.87[YRI][hapmap]
rs37974	0.90[YRI][hapmap]
rs37975	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs37977	1.00[CEU][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs37981	1.00[CEU][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs37988	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs37992	0.81[EUR][1000 genomes]
rs37994	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs37995	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs37997	0.89[YRI][hapmap]
rs37998	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs37999	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs38001	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs38002	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs38003	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs38004	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38006	0.82[EUR][1000 genomes]
rs38010	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs38011	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38012	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs38013	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38014	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38016	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38017	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38018	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs38019	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38021	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs38022	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs38023	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4140809	0.83[YRI][hapmap]
rs4236406	0.93[YRI][hapmap]
rs4720761	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4725057	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4725065	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4725068	0.86[YRI][hapmap]
rs62433404	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7785493	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9692283	0.93[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[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
rs4725060	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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