Variant report

Variant	rs10770073
Chromosome Location	chr11:9917968-9917969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10743120	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10770070	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10770072	0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs10840316	0.89[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs10840319	0.86[EUR][1000 genomes]
rs10840320	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs10840322	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11042527	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11042531	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11042532	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11042540	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs11042541	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12362504	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12800780	0.94[JPT][hapmap]
rs4910073	0.96[ASN][1000 genomes]
rs4910074	0.96[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55813311	0.98[ASN][1000 genomes]
rs56138865	0.98[ASN][1000 genomes]
rs56165961	0.97[ASN][1000 genomes]
rs6483805	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6483809	0.83[LWK][hapmap];0.84[AFR][1000 genomes]
rs7105337	0.87[LWK][hapmap];0.82[MKK][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes]
rs7119074	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs7130681	0.80[YRI][hapmap]
rs7130923	0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs71463738	0.93[ASN][1000 genomes]
rs7931062	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7936793	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7949582	0.92[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7950655	0.83[YRI][hapmap]
rs9300099	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9300100	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9332432	0.81[CEU][hapmap];0.80[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9919608	0.83[AFR][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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv2762895	chr11:9849511-9954549	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv896988	chr11:9912052-10012511	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10770073	LMO1	cis	parietal	SCAN
rs10770073	OR10A4	cis	cerebellum	SCAN
rs10770073	PTH	cis	cerebellum	SCAN
rs10770073	SWAP70	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9878800-9952200	Weak transcription	Aorta	Aorta
2	chr11:9882400-9929600	Weak transcription	Primary T cells from cord blood	blood
3	chr11:9892400-9921200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:9894400-9978600	Weak transcription	Left Ventricle	heart
5	chr11:9904000-9937000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:9906800-9920400	Weak transcription	HUVEC	blood vessel
7	chr11:9910000-9954600	Weak transcription	Pancreas	Pancrea
8	chr11:9910200-9921000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr11:9911600-9919200	Weak transcription	Fetal Brain Female	brain
10	chr11:9911800-9921200	Weak transcription	HMEC	breast
11	chr11:9913400-9919800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr11:9913400-9921000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr11:9913600-9921200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:9913600-9928800	Weak transcription	Right Ventricle	heart
15	chr11:9913800-9927400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:9914200-9926800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr11:9914400-9927600	Weak transcription	Brain Anterior Caudate	brain
18	chr11:9915000-9918600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:9915000-9921000	Weak transcription	Hela-S3	cervix
20	chr11:9915000-9937200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr11:9915200-9922600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:9915400-9921400	Weak transcription	NHLF	lung
23	chr11:9915400-9923200	Weak transcription	HSMMtube	muscle
24	chr11:9915400-9926800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr11:9915400-9927600	Weak transcription	Colon Smooth Muscle	Colon
26	chr11:9915600-9921200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr11:9915600-9923400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr11:9915800-9923000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:9916400-9918400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr11:9916600-9919000	Weak transcription	Fetal Stomach	stomach
31	chr11:9916600-9921400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr11:9916600-9923000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:9916600-9925200	Weak transcription	Lung	lung
34	chr11:9916600-9932600	Weak transcription	Fetal Intestine Small	intestine
35	chr11:9916800-9918200	Weak transcription	Fetal Muscle Leg	muscle
36	chr11:9916800-9921000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr11:9916800-9921800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:9916800-9922800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr11:9916800-9923600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr11:9916800-9925000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr11:9916800-9944400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr11:9916800-9944400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr11:9917000-9923800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:9917000-9927600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr11:9917000-9937200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr11:9917200-9922800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr11:9917200-9923000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr11:9917200-9925000	Weak transcription	Ovary	ovary
49	chr11:9917200-9927400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:9917400-9920200	Weak transcription	Rectal Mucosa Donor 29	rectum

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