Variant report

Variant	rs2290469
Chromosome Location	chr8:99029904-99029905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:99028352..99031100-chr8:99051141..99054386,3	MCF-7	breast:
2	chr8:99028962..99031053-chr8:99042963..99045444,2	MCF-7	breast:
3	chr8:99024327..99027909-chr8:99029199..99033016,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132561	Chromatin interaction
ENSG00000245970	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10098159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955140	0.85[CEU][hapmap]
rs10955141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955142	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955143	0.85[CEU][hapmap]
rs10955145	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10955146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955147	0.86[ASN][1000 genomes]
rs11559201	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11559202	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11776602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11777189	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11784449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11785807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11990341	0.83[ASN][1000 genomes]
rs11991161	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11996042	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11997426	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12544193	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12549802	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12549967	1.00[ASN][1000 genomes]
rs12550104	1.00[ASN][1000 genomes]
rs13248865	1.00[ASN][1000 genomes]
rs13254615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13254737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13255477	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13265127	1.00[ASN][1000 genomes]
rs13268951	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13269757	0.91[EUR][1000 genomes]
rs13270713	0.82[CEU][hapmap]
rs13274382	1.00[ASN][1000 genomes]
rs13279197	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13439743	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16896517	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17829645	1.00[JPT][hapmap]
rs2279120	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2290467	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2290468	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3088121	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34139241	1.00[ASN][1000 genomes]
rs34276726	1.00[ASN][1000 genomes]
rs34899856	1.00[ASN][1000 genomes]
rs35170774	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35417638	1.00[ASN][1000 genomes]
rs3758031	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55779959	1.00[ASN][1000 genomes]
rs56137923	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57866232	1.00[ASN][1000 genomes]
rs60324498	1.00[ASN][1000 genomes]
rs68116021	0.83[ASN][1000 genomes]
rs68131553	1.00[ASN][1000 genomes]
rs6985709	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6986891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7004993	1.00[ASN][1000 genomes]
rs7012838	1.00[ASN][1000 genomes]
rs7016999	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71514975	1.00[ASN][1000 genomes]
rs72678742	1.00[ASN][1000 genomes]
rs812	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2290469	KB-1208A12.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99008400-99045000	Weak transcription	Colonic Mucosa	Colon
2	chr8:99009000-99030000	Weak transcription	Pancreas	Pancrea
3	chr8:99009000-99030200	Weak transcription	Esophagus	oesophagus
4	chr8:99012000-99032000	Weak transcription	Gastric	stomach
5	chr8:99015000-99034400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr8:99019000-99033200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr8:99020000-99033400	Weak transcription	Left Ventricle	heart
8	chr8:99021000-99032200	Weak transcription	Brain Substantia Nigra	brain
9	chr8:99021200-99032800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr8:99021200-99053600	Weak transcription	A549	lung
11	chr8:99021400-99033400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr8:99021400-99043800	Weak transcription	Brain Germinal Matrix	brain
13	chr8:99022400-99055200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr8:99023000-99033400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr8:99023200-99030000	Weak transcription	Fetal Intestine Small	intestine
16	chr8:99023600-99034800	Strong transcription	Placenta Amnion	Placenta Amnion
17	chr8:99023800-99041200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr8:99024000-99030000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr8:99024000-99030000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr8:99024000-99030200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr8:99024000-99032800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr8:99024000-99044000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr8:99024000-99054800	Weak transcription	Right Ventricle	heart
24	chr8:99024200-99030000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr8:99024200-99032800	Weak transcription	Colon Smooth Muscle	Colon
26	chr8:99024200-99033200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr8:99024200-99033200	Weak transcription	NHDF-Ad	bronchial
28	chr8:99024200-99033600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr8:99024200-99042800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr8:99024200-99055000	Weak transcription	Fetal Brain Male	brain
31	chr8:99024200-99056000	Weak transcription	Spleen	Spleen
32	chr8:99024400-99032800	Weak transcription	HSMMtube	muscle
33	chr8:99024600-99030000	Weak transcription	Fetal Lung	lung
34	chr8:99025000-99030600	Strong transcription	Fetal Muscle Trunk	muscle
35	chr8:99025000-99052800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr8:99025200-99030000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr8:99025200-99030000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr8:99025200-99045400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr8:99025400-99030000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr8:99025400-99032600	Strong transcription	Fetal Stomach	stomach
41	chr8:99025400-99045200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr8:99026000-99033200	Weak transcription	NHLF	lung
43	chr8:99026800-99033400	Weak transcription	Small Intestine	intestine
44	chr8:99026800-99036600	Weak transcription	Lung	lung
45	chr8:99027200-99031000	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr8:99027200-99031400	Weak transcription	Dnd41	blood
47	chr8:99027400-99030000	Weak transcription	Primary B cells from cord blood	blood
48	chr8:99027400-99032200	Strong transcription	Fetal Muscle Leg	muscle
49	chr8:99027600-99030000	Strong transcription	Duodenum Mucosa	Duodenum
50	chr8:99027600-99037400	Weak transcription	Primary B cells from peripheral blood	blood

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