Variant report

Variant	rs11992703
Chromosome Location	chr8:19538810-19538811
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:19536477..19540083-chr8:19612902..19617470,5	MCF-7	breast:
2	chr8:19535157..19537582-chr8:19537640..19539899,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253270	Chromatin interaction
ENSG00000147408	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10087146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10107740	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10112417	0.85[AMR][1000 genomes]
rs1021436	0.83[AMR][1000 genomes]
rs12056388	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13253689	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1552777	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1552782	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17481200	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs17481221	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs3735956	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4244455	0.82[CHB][hapmap]
rs4548199	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4921669	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4922081	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4922082	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4922083	0.88[ASN][1000 genomes]
rs4922090	0.84[AMR][1000 genomes]
rs7016714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7016838	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7833352	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7836255	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv890625	chr8:19368697-19799641	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv890627	chr8:19389865-19561997	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1021575	chr8:19430653-19623452	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1025271	chr8:19435147-19574969	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv6106	chr8:19499554-19544249	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1021731	chr8:19515149-19643313	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv890628	chr8:19527536-19540966	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv465602	chr8:19536015-19555398	Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv610757	chr8:19536015-19555398	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv465603	chr8:19537084-19555398	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv465604	chr8:19537084-19555398	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv465606	chr8:19537084-19555398	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv465607	chr8:19537084-19555398	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv470203	chr8:19537084-19555398	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv610758	chr8:19537084-19555398	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11992703	CSGALNACT1	cis	Whole Blood	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19520400-19539000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr8:19520400-19539400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr8:19520400-19539600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr8:19523800-19540200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr8:19524200-19539000	Weak transcription	Ovary	ovary
6	chr8:19528600-19540200	Weak transcription	Spleen	Spleen
7	chr8:19532000-19539200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr8:19533800-19539000	Weak transcription	Thymus	Thymus
9	chr8:19534400-19539000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr8:19534600-19539200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr8:19536000-19539200	Weak transcription	Fetal Lung	lung
12	chr8:19536200-19539200	Weak transcription	NHLF	lung
13	chr8:19536200-19540800	Enhancers	Pancreas	Pancrea
14	chr8:19536400-19539000	Weak transcription	Stomach Mucosa	stomach
15	chr8:19536400-19539600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr8:19536400-19539600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr8:19536400-19543600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr8:19536600-19539600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr8:19536600-19539600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr8:19536800-19539600	Weak transcription	HepG2	liver
21	chr8:19537400-19540200	Enhancers	Hela-S3	cervix
22	chr8:19537600-19539000	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr8:19537600-19540200	Weak transcription	Brain Substantia Nigra	brain
24	chr8:19537600-19541000	Genic enhancers	A549	lung
25	chr8:19538000-19540200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr8:19538400-19539200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr8:19538400-19539800	Enhancers	Placenta	Placenta
28	chr8:19538400-19539800	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr8:19538400-19540000	Enhancers	Primary B cells from cord blood	blood
30	chr8:19538400-19541200	Enhancers	Fetal Heart	heart
31	chr8:19538400-19541400	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr8:19538600-19539200	Enhancers	Brain Hippocampus Middle	brain
33	chr8:19538600-19539400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr8:19538600-19539600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr8:19538600-19539600	Enhancers	Brain Anterior Caudate	brain
36	chr8:19538600-19539800	Enhancers	Left Ventricle	heart
37	chr8:19538600-19540000	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr8:19538600-19540000	Enhancers	Right Atrium	heart
39	chr8:19538600-19540600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr8:19538600-19541000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr8:19538800-19539000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr8:19538800-19539000	Enhancers	Primary T cells from cord blood	blood
43	chr8:19538800-19539400	Enhancers	Osteobl	bone
44	chr8:19538800-19539600	Enhancers	Right Ventricle	heart
45	chr8:19538800-19540400	Enhancers	Esophagus	oesophagus
46	chr8:19538800-19540600	Enhancers	Fetal Thymus	thymus
47	chr8:19538800-19540600	Enhancers	Gastric	stomach
48	chr8:19538800-19540800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr8:19538800-19540800	Enhancers	Lung	lung
50	chr8:19538800-19541000	Enhancers	Primary monocytes fromperipheralblood	blood

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