Variant report

Variant	rs2840958
Chromosome Location	chr1:225805043-225805044
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225798177..225800708-chr1:225805039..225808284,3	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10753406	0.83[EUR][1000 genomes]
rs10799316	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap]
rs10799317	0.83[EUR][1000 genomes]
rs10799318	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10799319	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10915828	0.93[CHB][hapmap]
rs10915833	0.83[EUR][1000 genomes]
rs10915834	0.81[EUR][1000 genomes]
rs10915839	0.83[EUR][1000 genomes]
rs10915847	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11584675	0.83[EUR][1000 genomes]
rs12028305	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1222440	0.83[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap]
rs2639703	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];0.84[MKK][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2639716	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2657564	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2657569	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2840967	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2840968	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3820226	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3856156	0.83[EUR][1000 genomes]
rs4653643	0.94[CEU][hapmap];0.94[CHB][hapmap];0.83[EUR][1000 genomes]
rs476540	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs487591	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs498350	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs510293	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs511649	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs516249	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs551996	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs554744	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs554992	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs561656	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs576861	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6426076	0.83[EUR][1000 genomes]
rs6668770	0.83[EUR][1000 genomes]
rs6697783	0.94[CHB][hapmap]
rs6702555	0.80[EUR][1000 genomes]
rs6751	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs712062	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7515907	0.83[EUR][1000 genomes]
rs7524766	0.83[EUR][1000 genomes]
rs7540181	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7541598	0.83[EUR][1000 genomes]
rs7555139	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7555553	0.83[EUR][1000 genomes]
rs812523	0.84[ASN][1000 genomes]
rs9804142	0.83[EUR][1000 genomes]

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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2840958	C1orf109	trans	brain	seeQTL
rs2840958	USP10	trans	brain	seeQTL
rs2840958	RP11-496N12.9	cis	Thyroid	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225760000-225820600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:225768800-225805600	Weak transcription	Aorta	Aorta
3	chr1:225780800-225815400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:225781000-225825400	Weak transcription	Fetal Stomach	stomach
5	chr1:225782400-225806200	Weak transcription	Right Ventricle	heart
6	chr1:225784200-225807800	Weak transcription	Fetal Brain Male	brain
7	chr1:225793600-225813200	Weak transcription	Left Ventricle	heart
8	chr1:225793600-225813800	Weak transcription	NH-A	brain
9	chr1:225794600-225813200	Weak transcription	Lung	lung
10	chr1:225795000-225806000	Weak transcription	Small Intestine	intestine
11	chr1:225795600-225805400	Weak transcription	NHLF	lung
12	chr1:225795600-225813200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:225795600-225813200	Weak transcription	Psoas Muscle	Psoas
14	chr1:225795600-225813800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:225796400-225810200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:225796400-225812600	Weak transcription	Right Atrium	heart
17	chr1:225796600-225812200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:225797200-225806200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:225797200-225815200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:225797400-225812600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:225797400-225814000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:225798800-225806200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:225798800-225808800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:225800200-225805200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:225800200-225812600	Weak transcription	Gastric	stomach
26	chr1:225800400-225805600	Weak transcription	Adipose Nuclei	Adipose
27	chr1:225801000-225805400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:225801200-225806000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:225801200-225806000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:225801600-225809600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:225801600-225813600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:225802400-225805800	Weak transcription	Ovary	ovary
33	chr1:225802600-225805200	Weak transcription	Osteobl	bone
34	chr1:225802600-225805400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:225802600-225805400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr1:225802600-225805600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:225802600-225805800	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:225802600-225809800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:225802600-225813400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:225802600-225813800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:225802800-225805400	Weak transcription	Brain Hippocampus Middle	brain
42	chr1:225802800-225811600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:225803800-225806800	Enhancers	A549	lung
44	chr1:225804000-225805600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:225804400-225807000	Enhancers	Colon Smooth Muscle	Colon
46	chr1:225804600-225806800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:225804600-225806800	Enhancers	Rectal Smooth Muscle	rectum
48	chr1:225804600-225809800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:225804800-225805200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:225804800-225806200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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