Variant report

Variant	rs1946940
Chromosome Location	chr8:87558283-87558284
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:87551519..87555405-chr8:87558017..87562987,4	MCF-7	breast:
2	chr8:87519168..87522025-chr8:87556518..87558633,2	MCF-7	breast:
3	chr8:87526686..87529594-chr8:87554156..87558749,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085719	Chromatin interaction
ENSG00000176623	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10087788	0.82[JPT][hapmap]
rs10088389	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10088739	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs10092164	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10093238	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10095129	0.82[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10096443	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10956853	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1142528	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs11775728	0.87[CHB][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap]
rs11781016	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11787318	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs12543856	0.83[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs12546331	0.92[CEU][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13251647	0.86[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs17608967	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs1946939	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213911	0.86[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs3213912	0.82[JPT][hapmap]
rs3883910	0.83[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3903247	0.82[EUR][1000 genomes]
rs4961190	0.83[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs4961194	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4961196	0.93[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56122533	0.82[EUR][1000 genomes]
rs56321721	0.82[EUR][1000 genomes]
rs62510806	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62510845	0.82[EUR][1000 genomes]
rs6415565	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6471349	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6471351	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6471352	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6471354	0.88[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6651267	0.82[JPT][hapmap]
rs6981299	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6988601	0.81[ASN][1000 genomes]
rs6994005	0.82[CEU][hapmap]
rs6996052	0.82[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs6999022	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7006017	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap]
rs7006629	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7015263	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7459811	0.93[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7459897	0.93[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7460251	0.81[CEU][hapmap]
rs7460439	0.82[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7461624	0.86[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs7463186	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7465350	0.85[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs7817738	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7818213	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7820697	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7822494	0.81[ASN][1000 genomes]
rs7823154	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9642913	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs9773093	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349873	chr8:87185763-87603726	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1023510	chr8:87429001-87874948	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv933966	chr8:87454655-87591558	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1946940	FAM82B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87527400-87568400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:87527600-87562000	Weak transcription	Pancreas	Pancrea
3	chr8:87527600-87568200	Weak transcription	Gastric	stomach
4	chr8:87527600-87584000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr8:87527800-87560000	Weak transcription	HSMMtube	muscle
6	chr8:87528000-87563800	Weak transcription	Hela-S3	cervix
7	chr8:87528000-87573600	Weak transcription	Stomach Mucosa	stomach
8	chr8:87528200-87572000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr8:87528400-87560400	Weak transcription	Thymus	Thymus
10	chr8:87528600-87566000	Weak transcription	Spleen	Spleen
11	chr8:87536000-87559400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr8:87539600-87560200	Weak transcription	Lung	lung
13	chr8:87541600-87563800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr8:87541600-87570600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr8:87542000-87558800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr8:87543200-87571200	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr8:87543200-87572600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr8:87543400-87568800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr8:87543800-87560000	Weak transcription	Esophagus	oesophagus
20	chr8:87545000-87571400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr8:87545000-87576800	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr8:87546400-87569400	Strong transcription	NHDF-Ad	bronchial
23	chr8:87546600-87570200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr8:87546600-87570800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr8:87547800-87563200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr8:87548400-87569400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr8:87548800-87573400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr8:87549000-87572600	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr8:87549200-87568200	Weak transcription	K562	blood
30	chr8:87549800-87566000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr8:87550600-87560400	Weak transcription	Aorta	Aorta
32	chr8:87550600-87569800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr8:87550800-87560400	Weak transcription	Fetal Stomach	stomach
34	chr8:87551000-87559400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr8:87551200-87559400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr8:87551200-87559600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr8:87551200-87568200	Weak transcription	Psoas Muscle	Psoas
38	chr8:87551600-87559600	Weak transcription	HepG2	liver
39	chr8:87551600-87560000	Weak transcription	Right Ventricle	heart
40	chr8:87552200-87561800	Weak transcription	Fetal Intestine Small	intestine
41	chr8:87552600-87575000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr8:87553000-87559600	Weak transcription	NH-A	brain
43	chr8:87553000-87572800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr8:87553800-87575000	Strong transcription	Primary B cells from cord blood	blood
45	chr8:87554600-87566000	Weak transcription	Fetal Heart	heart
46	chr8:87555400-87560800	Strong transcription	GM12878-XiMat	blood
47	chr8:87555600-87567600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr8:87555600-87571400	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr8:87555600-87571600	Strong transcription	Primary B cells from peripheral blood	blood
50	chr8:87555600-87572800	Strong transcription	Monocytes-CD14+_RO01746	blood

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