Variant report

Variant	rs6478131
Chromosome Location	chr9:100140742-100140743
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	chr9:100139724..100142040-chr9:100160057..100161608,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TDRD7-1	chr9:100137736-100140806	NONHSAT133501

Extended variants
information (count: 63 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10122063	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10125198	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1020884	0.95[EUR][1000 genomes]
rs1020885	0.95[EUR][1000 genomes]
rs1037948	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1037950	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1037951	0.94[EUR][1000 genomes]
rs10435867	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10435868	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10448274	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759624	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10759657	0.95[EUR][1000 genomes]
rs10817487	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10981890	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10981919	0.95[EUR][1000 genomes]
rs10981931	0.93[EUR][1000 genomes]
rs11581	0.81[ASN][1000 genomes]
rs1542506	0.93[EUR][1000 genomes]
rs1544203	0.81[ASN][1000 genomes]
rs1903635	0.81[ASN][1000 genomes]
rs1947717	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2219664	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2242187	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306097	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2493442	0.82[ASN][1000 genomes]
rs2493443	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2502644	0.81[ASN][1000 genomes]
rs2615143	0.81[ASN][1000 genomes]
rs2615145	0.81[ASN][1000 genomes]
rs2795365	0.82[ASN][1000 genomes]
rs2795367	0.82[ASN][1000 genomes]
rs2818238	0.82[ASN][1000 genomes]
rs2818239	0.80[ASN][1000 genomes]
rs2818243	0.81[ASN][1000 genomes]
rs3214072	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs34955252	0.81[ASN][1000 genomes]
rs35609998	0.81[ASN][1000 genomes]
rs3747489	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3747493	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3747496	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3802471	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4237189	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4313271	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4366181	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4523384	0.81[ASN][1000 genomes]
rs4523385	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4554595	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4742685	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4742689	0.95[EUR][1000 genomes]
rs4742690	0.95[EUR][1000 genomes]
rs4743072	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4743076	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4743077	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743084	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743088	0.95[EUR][1000 genomes]
rs6478095	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs713066	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs750674	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7856924	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7869536	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9696167	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036105	chr9:100131266-100171816	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6478131	VN1R51P	cis	Thyroid	GTEx
rs6478131	ANKRD18CP	cis	Thyroid	GTEx
rs6478131	RP11-520B13.4	cis	Thyroid	GTEx
rs6478131	RP11-520B13.4	cis	Esophagus Muscularis	GTEx
rs6478131	RP11-498P14.5	cis	lung	GTEx

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100077000-100140800	Weak transcription	Fetal Brain Male	brain
2	chr9:100091600-100149200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr9:100104400-100142000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:100106800-100143200	Weak transcription	Liver	Liver
5	chr9:100108000-100148200	Weak transcription	Esophagus	oesophagus
6	chr9:100115400-100144600	Weak transcription	Hela-S3	cervix
7	chr9:100117400-100145000	Weak transcription	Colon Smooth Muscle	Colon
8	chr9:100117600-100146400	Weak transcription	Small Intestine	intestine
9	chr9:100118200-100141600	Weak transcription	Primary T cells from cord blood	blood
10	chr9:100126600-100141600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr9:100126600-100148400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:100127000-100148600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr9:100129000-100144400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr9:100132000-100142600	Weak transcription	Fetal Kidney	kidney
15	chr9:100132000-100149000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr9:100132200-100141000	Strong transcription	Stomach Smooth Muscle	stomach
17	chr9:100132200-100141400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr9:100132400-100141000	Strong transcription	Adipose Nuclei	Adipose
19	chr9:100132400-100146800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr9:100132600-100144400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:100132600-100146800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:100132600-100148600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:100132600-100149400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr9:100132600-100149400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:100132800-100141200	Strong transcription	Fetal Stomach	stomach
26	chr9:100133000-100141000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:100133400-100148400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:100134000-100142200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr9:100134000-100144400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:100134600-100148600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:100135800-100141200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr9:100136000-100141400	Strong transcription	Brain Hippocampus Middle	brain
33	chr9:100136000-100142400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr9:100136600-100142800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr9:100136600-100148000	Weak transcription	Colonic Mucosa	Colon
36	chr9:100137000-100141400	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr9:100137200-100141000	Strong transcription	Brain Anterior Caudate	brain
38	chr9:100137800-100140800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr9:100137800-100141000	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr9:100137800-100141200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr9:100137800-100141200	Strong transcription	Lung	lung
42	chr9:100138400-100140800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr9:100138600-100140800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr9:100138600-100146000	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr9:100138800-100141000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr9:100139400-100141400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr9:100139400-100144000	Weak transcription	Fetal Muscle Leg	muscle
48	chr9:100139400-100145000	Weak transcription	Gastric	stomach
49	chr9:100139400-100146200	Weak transcription	Aorta	Aorta
50	chr9:100139400-100148400	Weak transcription	Pancreas	Pancrea

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