Variant report

Variant	rs4725065
Chromosome Location	chr7:8109522-8109523
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10215645	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10226050	0.80[JPT][hapmap]
rs10228900	0.83[ASN][1000 genomes]
rs10229643	0.81[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs10231036	0.81[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs10241457	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10243846	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10247928	0.85[ASN][1000 genomes]
rs10248588	0.87[ASN][1000 genomes]
rs10253861	0.81[CEU][hapmap]
rs10258788	0.82[ASN][1000 genomes]
rs10273241	0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10278726	0.88[CEU][hapmap]
rs10486205	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs10486207	0.81[ASN][1000 genomes]
rs11984078	0.84[ASN][1000 genomes]
rs12702692	0.93[ASN][1000 genomes]
rs12702693	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17568389	0.96[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2079853	0.95[ASN][1000 genomes]
rs2109382	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2191321	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2348774	0.84[ASN][1000 genomes]
rs258853	0.82[ASN][1000 genomes]
rs37981	0.91[JPT][hapmap]
rs37988	1.00[JPT][hapmap]
rs37995	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs37997	0.92[CEU][hapmap];0.87[AMR][1000 genomes]
rs37998	1.00[JPT][hapmap]
rs37999	1.00[JPT][hapmap]
rs38002	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs38003	1.00[JPT][hapmap]
rs38004	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs38007	0.91[CEU][hapmap]
rs38011	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs38012	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs38013	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs38014	1.00[JPT][hapmap]
rs38016	0.82[ASN][1000 genomes]
rs38018	0.87[CHB][hapmap];0.92[JPT][hapmap]
rs38019	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs38021	0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs38022	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs4236406	0.82[AFR][1000 genomes]
rs4256496	0.81[CEU][hapmap]
rs4720761	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4725057	0.84[ASN][1000 genomes]
rs4725060	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7785493	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7796831	0.81[CEU][hapmap]
rs9692283	0.94[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv519058	chr7:8094604-8115794	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1020686	chr7:8095118-8311985	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv538723	chr7:8095118-8311985	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	esv1009766	chr7:8106112-8134286	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4725065	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8066400-8127600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr7:8066600-8126000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr7:8067000-8135400	Weak transcription	Pancreas	Pancrea
4	chr7:8075000-8125800	Weak transcription	Lung	lung
5	chr7:8075000-8126800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:8075600-8113000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:8075600-8131800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr7:8076000-8111800	Weak transcription	Fetal Brain Male	brain
9	chr7:8076000-8124200	Weak transcription	Fetal Kidney	kidney
10	chr7:8085200-8128400	Weak transcription	Small Intestine	intestine
11	chr7:8091400-8127800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr7:8094000-8127800	Weak transcription	HSMM	muscle
13	chr7:8095200-8125800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr7:8095400-8129600	Weak transcription	Gastric	stomach
15	chr7:8096000-8125800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr7:8096000-8127600	Weak transcription	Esophagus	oesophagus
17	chr7:8096000-8151600	Weak transcription	Spleen	Spleen
18	chr7:8097200-8114400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr7:8097400-8124600	Weak transcription	Fetal Intestine Large	intestine
20	chr7:8099200-8113200	Strong transcription	Primary B cells from cord blood	blood
21	chr7:8100400-8124600	Weak transcription	Liver	Liver
22	chr7:8100600-8112800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr7:8100800-8125000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr7:8102400-8110400	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr7:8102400-8111800	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr7:8102600-8111800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr7:8102800-8110400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr7:8102800-8130000	Weak transcription	Fetal Lung	lung
29	chr7:8103000-8124600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr7:8103000-8125200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr7:8103000-8127800	Weak transcription	Fetal Brain Female	brain
32	chr7:8103000-8128000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr7:8103000-8135400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr7:8103200-8110400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr7:8103200-8131400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr7:8103400-8110200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr7:8103400-8110400	Weak transcription	Placenta	Placenta
38	chr7:8103600-8110200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:8103600-8110400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr7:8103600-8110400	Weak transcription	Ovary	ovary
41	chr7:8103600-8114800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:8103800-8110200	Weak transcription	Hela-S3	cervix
43	chr7:8104600-8125200	Weak transcription	Aorta	Aorta
44	chr7:8105400-8110400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr7:8105400-8110600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr7:8105600-8115400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr7:8105800-8110400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr7:8106000-8110600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr7:8106000-8126000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr7:8106200-8126200	Weak transcription	Muscle Satellite Cultured Cells	--

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