Variant report

Variant	rs7931260
Chromosome Location	chr11:47088303-47088304
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10466478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10501319	0.83[CHB][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap]
rs1055447	0.81[GIH][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1060573	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10769225	0.82[CHB][hapmap]
rs10769226	0.83[CHB][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap]
rs10769227	0.83[CHB][hapmap]
rs10769230	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10769233	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10769234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10769239	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10838635	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs10838640	0.83[CHB][hapmap]
rs10838644	0.83[CHB][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap]
rs10838646	0.83[CHB][hapmap]
rs10838652	0.83[CHB][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs10838654	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10838658	0.82[CHB][hapmap]
rs10838659	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10838660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10838662	0.83[CHB][hapmap];0.92[GIH][hapmap];0.83[MEX][hapmap]
rs10838663	0.83[CHB][hapmap]
rs10838664	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs11039035	0.83[CHB][hapmap]
rs11039074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039086	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039097	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039105	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039107	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039112	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039119	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.87[ASN][1000 genomes]
rs11039124	0.84[ASN][1000 genomes]
rs11600292	0.83[CHB][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap]
rs11600668	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11601798	0.85[CHB][hapmap]
rs11602250	0.84[CHB][hapmap]
rs12224096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12273333	0.84[YRI][hapmap]
rs12417519	0.83[CHB][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs12574410	0.86[CHB][hapmap]
rs12796744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12807887	0.84[ASN][1000 genomes]
rs17790204	0.82[CHB][hapmap]
rs1872896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1965952	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2018527	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2029298	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap]
rs2087215	0.83[CHB][hapmap];0.92[GIH][hapmap]
rs2279438	0.83[CHB][hapmap]
rs2279439	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs4319472	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4394802	0.94[GIH][hapmap];0.82[MEX][hapmap]
rs4528282	0.82[CHB][hapmap]
rs4548577	0.83[CHB][hapmap]
rs4567413	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs4579897	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4581406	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs4587689	0.83[CHB][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs4752815	0.83[CHB][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs4752816	0.83[CHB][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs4752951	0.82[CHB][hapmap]
rs4752952	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4752957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4752962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4752963	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4752965	0.83[CHB][hapmap]
rs4752967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4752969	0.83[CHB][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap]
rs4752971	0.95[CEU][hapmap];0.84[ASN][1000 genomes]
rs57323109	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6485702	0.86[CHD][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap]
rs6485715	0.83[CHB][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs6485716	0.86[CHB][hapmap]
rs6485721	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6485722	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6485726	0.83[CHB][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs6485739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7103581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7108902	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7111270	0.83[CHB][hapmap]
rs7112854	0.82[CHB][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs7118546	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7119952	0.81[ASN][1000 genomes]
rs7121418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7124648	0.83[CHB][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs7125807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7126005	0.83[CHB][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs7128325	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7128650	0.83[CHB][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs7130006	0.83[CHB][hapmap];0.83[GIH][hapmap]
rs7130947	0.83[CHB][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs747650	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7479189	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7935346	0.94[GIH][hapmap]
rs7937101	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap]
rs7937410	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7937950	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7938169	0.83[CHB][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs7940240	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7940441	0.86[GIH][hapmap]
rs7942473	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7945315	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7945558	0.83[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap]
rs7946709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7947878	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7950753	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs923324	0.82[CHB][hapmap]
rs9633886	0.82[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	nsv1043108	chr11:47041565-47117248	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7931260	CTD-2384B9.1	cis	Nerve Tibial	GTEx
rs7931260	F2	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47068400-47092400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr11:47071600-47089000	Weak transcription	Gastric	stomach
3	chr11:47072600-47093000	Weak transcription	Ovary	ovary
4	chr11:47072800-47093000	Weak transcription	Brain Hippocampus Middle	brain
5	chr11:47073200-47092400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:47073600-47088600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr11:47073800-47092200	Weak transcription	Placenta	Placenta
8	chr11:47073800-47100200	Weak transcription	Thymus	Thymus
9	chr11:47075200-47093400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:47075800-47093400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr11:47077600-47113200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:47078000-47097000	Weak transcription	Aorta	Aorta
13	chr11:47078200-47093200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr11:47078400-47092400	Weak transcription	Small Intestine	intestine
15	chr11:47078600-47092600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr11:47079400-47093000	Weak transcription	Fetal Brain Male	brain
17	chr11:47080000-47092400	Weak transcription	Fetal Intestine Small	intestine
18	chr11:47080000-47092400	Weak transcription	Fetal Stomach	stomach
19	chr11:47080400-47090000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:47080600-47093200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr11:47080800-47103000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:47081000-47092400	Weak transcription	Fetal Intestine Large	intestine
23	chr11:47081200-47089000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:47083000-47088400	Weak transcription	NHLF	lung
25	chr11:47083200-47089000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:47083200-47093000	Weak transcription	Brain Anterior Caudate	brain
27	chr11:47083200-47093000	Weak transcription	Brain Substantia Nigra	brain
28	chr11:47083200-47100600	Weak transcription	NH-A	brain
29	chr11:47083400-47089000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr11:47083400-47091600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr11:47083600-47089000	Weak transcription	K562	blood
32	chr11:47083600-47092800	Weak transcription	A549	lung
33	chr11:47084000-47088400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:47084400-47088400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr11:47084400-47088400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr11:47084400-47090800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr11:47084600-47089000	Weak transcription	Fetal Muscle Leg	muscle
38	chr11:47084600-47092000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr11:47084600-47093000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr11:47084600-47093400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr11:47084600-47093400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr11:47084600-47093400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr11:47084600-47093400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr11:47084600-47098400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr11:47084800-47088400	Weak transcription	HSMM	muscle
46	chr11:47084800-47088800	Weak transcription	HSMMtube	muscle
47	chr11:47085400-47092400	Weak transcription	Fetal Lung	lung
48	chr11:47085800-47102400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr11:47087800-47088600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr11:47087800-47089200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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