Variant report

Variant	rs4236406
Chromosome Location	chr7:8113751-8113752
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10215645	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10226050	0.82[CEU][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs10228900	0.81[AMR][1000 genomes]
rs10229643	0.93[YRI][hapmap];0.83[AMR][1000 genomes]
rs10231036	0.83[CEU][hapmap];0.86[AMR][1000 genomes]
rs10241457	0.82[CEU][hapmap];0.83[LWK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes]
rs10243846	0.86[YRI][hapmap];0.83[AMR][1000 genomes]
rs10246564	0.95[CEU][hapmap]
rs10248588	0.85[AMR][1000 genomes]
rs10258788	0.80[AMR][1000 genomes]
rs10273241	0.93[YRI][hapmap]
rs10486205	0.93[YRI][hapmap]
rs11976862	0.91[CEU][hapmap];0.85[LWK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs11984078	0.85[AMR][1000 genomes]
rs12702693	0.90[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes]
rs17568389	0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs2079853	0.80[AFR][1000 genomes]
rs2109382	0.87[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2191321	0.89[YRI][hapmap]
rs2348774	0.85[AMR][1000 genomes]
rs258853	0.80[AMR][1000 genomes]
rs28670736	0.81[AMR][1000 genomes]
rs3735457	0.95[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs37974	0.83[YRI][hapmap]
rs37975	0.82[AMR][1000 genomes]
rs37977	0.81[TSI][hapmap];0.82[YRI][hapmap]
rs37981	0.82[CEU][hapmap];0.84[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes]
rs37988	0.93[YRI][hapmap];0.83[AMR][1000 genomes]
rs37994	0.82[CEU][hapmap]
rs37995	0.82[CEU][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes]
rs37998	0.82[CEU][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes]
rs37999	0.81[YRI][hapmap];0.80[AMR][1000 genomes]
rs38001	0.84[AMR][1000 genomes]
rs38002	0.89[YRI][hapmap];0.81[AMR][1000 genomes]
rs38003	0.89[YRI][hapmap];0.81[AMR][1000 genomes]
rs38004	0.93[YRI][hapmap];0.84[AMR][1000 genomes]
rs38011	0.93[YRI][hapmap];0.82[AMR][1000 genomes]
rs38012	0.82[CEU][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes]
rs38013	0.82[CEU][hapmap];0.82[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs38014	0.93[YRI][hapmap];0.81[AMR][1000 genomes]
rs38016	0.80[AMR][1000 genomes]
rs38017	0.80[AMR][1000 genomes]
rs38018	0.82[CEU][hapmap];0.83[LWK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs38019	0.96[YRI][hapmap];0.84[AMR][1000 genomes]
rs38021	0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs38022	0.81[CEU][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes]
rs38023	0.81[AMR][1000 genomes]
rs4140809	0.85[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap]
rs4720761	0.82[CEU][hapmap];0.85[LWK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes]
rs4725057	0.85[AMR][1000 genomes]
rs4725060	0.93[YRI][hapmap]
rs4725065	0.82[AFR][1000 genomes]
rs4725068	0.86[CEU][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62433404	0.81[AMR][1000 genomes]
rs9692283	0.83[CEU][hapmap];0.89[YRI][hapmap];0.85[AMR][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
rs4236406	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 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	chr7:8075600-8131800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr7:8076000-8124200	Weak transcription	Fetal Kidney	kidney
8	chr7:8085200-8128400	Weak transcription	Small Intestine	intestine
9	chr7:8091400-8127800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr7:8094000-8127800	Weak transcription	HSMM	muscle
11	chr7:8095200-8125800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr7:8095400-8129600	Weak transcription	Gastric	stomach
13	chr7:8096000-8125800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr7:8096000-8127600	Weak transcription	Esophagus	oesophagus
15	chr7:8096000-8151600	Weak transcription	Spleen	Spleen
16	chr7:8097200-8114400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr7:8097400-8124600	Weak transcription	Fetal Intestine Large	intestine
18	chr7:8100400-8124600	Weak transcription	Liver	Liver
19	chr7:8100800-8125000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr7:8102800-8130000	Weak transcription	Fetal Lung	lung
21	chr7:8103000-8124600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr7:8103000-8125200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr7:8103000-8127800	Weak transcription	Fetal Brain Female	brain
24	chr7:8103000-8128000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr7:8103000-8135400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr7:8103200-8131400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr7:8103600-8114800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr7:8104600-8125200	Weak transcription	Aorta	Aorta
29	chr7:8105600-8115400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr7:8106000-8126000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr7:8106200-8126200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr7:8106600-8128200	Weak transcription	Osteobl	bone
33	chr7:8107000-8117400	Strong transcription	Dnd41	blood
34	chr7:8107200-8124200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr7:8107600-8126000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr7:8109000-8117400	Strong transcription	Fetal Thymus	thymus
37	chr7:8109000-8118200	Weak transcription	Brain Angular Gyrus	brain
38	chr7:8109000-8125000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr7:8109000-8128400	Weak transcription	Brain Substantia Nigra	brain
40	chr7:8109000-8131800	Weak transcription	Fetal Muscle Leg	muscle
41	chr7:8109000-8132800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr7:8109200-8113800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr7:8109200-8116600	Weak transcription	Psoas Muscle	Psoas
44	chr7:8109200-8119400	Strong transcription	GM12878-XiMat	blood
45	chr7:8109200-8124000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr7:8109200-8124200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr7:8109200-8124400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr7:8109200-8125800	Weak transcription	Fetal Stomach	stomach
49	chr7:8109200-8125800	Weak transcription	Left Ventricle	heart
50	chr7:8109200-8128400	Weak transcription	Brain Hippocampus Middle	brain

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