Variant report

Variant	rs7016592
Chromosome Location	chr8:19277735-19277736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:19277038..19281251-chr8:19291957..19296139,6	MCF-7	breast:
2	chr8:19277635..19279188-chr8:19612998..19615550,2	MCF-7	breast:
3	chr8:19275354..19278233-chr8:19280534..19283813,3	MCF-7	breast:
4	chr8:19277703..19280587-chr8:19673604..19675691,2	MCF-7	breast:
5	chr8:19244439..19246344-chr8:19276946..19278452,2	MCF-7	breast:
6	chr8:19275542..19277855-chr8:19280462..19282722,2	K562	blood:
7	chr8:19277716..19280530-chr8:19280967..19283858,2	MCF-7	breast:
8	chr8:19263579..19266063-chr8:19277722..19281368,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000104613	Chromatin interaction
ENSG00000147408	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10102696	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10107416	1.00[CEU][hapmap];0.84[CHB][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10481426	0.84[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10481427	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10481428	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11204039	1.00[CEU][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11204040	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11204041	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11778175	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11780343	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11780388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11782540	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11784873	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11785649	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11786847	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11787230	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11991105	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12542575	1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12543061	1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12674938	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12675717	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12678336	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12679671	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12679712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13255677	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13255946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13258090	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13278459	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17407039	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17479099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35029660	0.81[EUR][1000 genomes]
rs3802329	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4256608	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4333618	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4379462	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs4391454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4392915	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4392916	0.82[EUR][1000 genomes]
rs4409408	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs4412390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4430112	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4433156	1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4481612	0.83[CEU][hapmap];0.85[CHB][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes]
rs4546679	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4549789	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4554480	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4617172	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4618712	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4633071	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4642666	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4921638	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4921642	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6981898	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6983973	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6984145	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6990217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6990357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6991212	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6991231	0.99[ASN][1000 genomes]
rs6992893	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6992950	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6997164	0.85[AMR][1000 genomes]
rs6999786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7004435	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7006702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7011602	0.81[EUR][1000 genomes]
rs7015440	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7016259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7818345	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7821446	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7823194	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7833166	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7835461	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9720249	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015395	chr8:18489538-19370258	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv429907	chr8:18578720-19398220	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv949745	chr8:18826830-19363963	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1016482	chr8:18834807-19339487	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv533109	chr8:18845845-19456780	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1016993	chr8:18855623-19311731	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv610751	chr8:19226335-19284889	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
11	esv3693374	chr8:19241970-19359184	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
12	esv34007	chr8:19252602-19482098	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
13	nsv610752	chr8:19254816-19311496	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
14	nsv1022344	chr8:19270143-19324083	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7016592	CSGALNACT1	cis	Skin Sun Exposed Lower leg	GTEx
rs7016592	CSGALNACT1	cis	Thyroid	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19261800-19279600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr8:19266600-19283800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr8:19267000-19278400	Weak transcription	Esophagus	oesophagus
4	chr8:19267000-19279200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr8:19267200-19297000	Weak transcription	Brain Substantia Nigra	brain
6	chr8:19267400-19279400	Weak transcription	Adipose Nuclei	Adipose
7	chr8:19267400-19280800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr8:19267400-19281200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr8:19267400-19283600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr8:19267600-19281000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr8:19267800-19281800	Weak transcription	Brain Anterior Caudate	brain
12	chr8:19267800-19295600	Weak transcription	Brain Hippocampus Middle	brain
13	chr8:19268000-19279400	Weak transcription	Fetal Muscle Leg	muscle
14	chr8:19268000-19283800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr8:19270000-19279600	Strong transcription	Primary B cells from cord blood	blood
16	chr8:19270200-19288800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr8:19270400-19278800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr8:19270400-19283000	Weak transcription	Brain Angular Gyrus	brain
19	chr8:19271000-19284200	Weak transcription	Thymus	Thymus
20	chr8:19271400-19278600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr8:19271600-19281400	Weak transcription	Lung	lung
22	chr8:19271800-19279400	Weak transcription	Fetal Intestine Small	intestine
23	chr8:19271800-19281600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr8:19271800-19283400	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr8:19271800-19305200	Weak transcription	Pancreas	Pancrea
26	chr8:19272800-19281200	Weak transcription	Fetal Lung	lung
27	chr8:19273000-19277800	Strong transcription	Placenta	Placenta
28	chr8:19274000-19278600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr8:19274200-19278200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr8:19274800-19278200	Strong transcription	Left Ventricle	heart
31	chr8:19274800-19278600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr8:19274800-19279200	Enhancers	Placenta Amnion	Placenta Amnion
33	chr8:19274800-19280600	Strong transcription	Primary T cells from cord blood	blood
34	chr8:19275000-19277800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr8:19275000-19277800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr8:19275000-19278000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr8:19275000-19278000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr8:19275000-19278000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr8:19275000-19278600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr8:19275200-19278000	Strong transcription	Spleen	Spleen
41	chr8:19275800-19287200	Weak transcription	Gastric	stomach
42	chr8:19275800-19288600	Weak transcription	Aorta	Aorta
43	chr8:19275800-19295600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr8:19276200-19281400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr8:19276200-19281400	Weak transcription	Right Ventricle	heart
46	chr8:19276200-19283400	Weak transcription	Ovary	ovary
47	chr8:19276600-19278200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr8:19276800-19277800	Strong transcription	Primary B cells from peripheral blood	blood
49	chr8:19276800-19280400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr8:19277400-19283200	Strong transcription	A549	lung

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