Variant report

Variant	rs10818666
Chromosome Location	chr9:101006210-101006211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100993462..100999076-chr9:101001061..101006420,6	MCF-7	breast:
2	chr9:100818546..100820662-chr9:101005577..101007101,2	MCF-7	breast:
3	chr9:101005587..101007898-chr9:101011469..101013243,2	MCF-7	breast:
4	chr9:101000479..101004519-chr9:101004686..101007074,4	MCF-7	breast:
5	chr9:100683384..100686138-chr9:101006133..101008454,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136932	Chromatin interaction
ENSG00000095380	Chromatin interaction
ENSG00000224001	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10115971	0.90[ASN][1000 genomes]
rs10123643	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10124977	0.90[ASN][1000 genomes]
rs10760210	0.93[ASN][1000 genomes]
rs10760216	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760217	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760218	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818627	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818640	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818644	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818645	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818646	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818648	0.97[ASN][1000 genomes]
rs10818656	0.97[ASN][1000 genomes]
rs10818658	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818662	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818667	0.93[ASN][1000 genomes]
rs10818668	0.93[ASN][1000 genomes]
rs10818672	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818676	0.97[ASN][1000 genomes]
rs10818677	0.97[ASN][1000 genomes]
rs10818678	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818689	0.92[ASN][1000 genomes]
rs10818690	0.92[ASN][1000 genomes]
rs10818691	0.90[ASN][1000 genomes]
rs10818692	0.85[ASN][1000 genomes]
rs10818693	0.85[ASN][1000 genomes]
rs10985517	0.91[ASN][1000 genomes]
rs10985580	0.93[ASN][1000 genomes]
rs10985583	0.97[ASN][1000 genomes]
rs10985634	0.92[ASN][1000 genomes]
rs10985641	0.85[ASN][1000 genomes]
rs10985642	0.85[ASN][1000 genomes]
rs10985653	0.85[ASN][1000 genomes]
rs10985669	0.85[ASN][1000 genomes]
rs10985680	0.85[ASN][1000 genomes]
rs10985689	0.85[ASN][1000 genomes]
rs10985711	0.85[ASN][1000 genomes]
rs10985720	0.85[ASN][1000 genomes]
rs10985743	0.83[ASN][1000 genomes]
rs10985745	0.83[ASN][1000 genomes]
rs12237988	0.97[ASN][1000 genomes]
rs12342612	0.89[ASN][1000 genomes]
rs12346750	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573024	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573025	0.97[ASN][1000 genomes]
rs17766883	0.97[ASN][1000 genomes]
rs17766913	0.97[ASN][1000 genomes]
rs1935389	0.97[ASN][1000 genomes]
rs2900380	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4379551	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742719	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742721	0.85[ASN][1000 genomes]
rs4742722	0.85[ASN][1000 genomes]
rs4743187	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743188	0.93[ASN][1000 genomes]
rs4743192	0.97[ASN][1000 genomes]
rs4743194	0.93[ASN][1000 genomes]
rs56262782	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62574277	0.97[ASN][1000 genomes]
rs62574288	0.85[ASN][1000 genomes]
rs62574300	0.85[ASN][1000 genomes]
rs6478630	0.93[ASN][1000 genomes]
rs6478631	0.97[ASN][1000 genomes]
rs67569753	0.93[ASN][1000 genomes]
rs7025781	0.91[ASN][1000 genomes]
rs7032046	0.88[ASN][1000 genomes]
rs7042576	0.93[ASN][1000 genomes]
rs7045158	0.91[ASN][1000 genomes]
rs7853442	0.93[ASN][1000 genomes]
rs7853847	0.84[ASN][1000 genomes]
rs7859655	0.85[ASN][1000 genomes]
rs7868451	0.91[ASN][1000 genomes]
rs7873849	0.97[ASN][1000 genomes]
rs7874856	0.85[ASN][1000 genomes]
rs879368	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879369	0.93[ASN][1000 genomes]
rs9802650	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1810342	chr9:100995758-101006339	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
6	esv1807264	chr9:101000545-101006339	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
7	esv1810101	chr9:101000545-101006339	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10818666	TBC1D2	cis	Thyroid	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100968600-101010400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr9:100968800-101011000	Weak transcription	Primary B cells from peripheral blood	blood
3	chr9:100974800-101010600	Weak transcription	Colon Smooth Muscle	Colon
4	chr9:100980200-101010200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr9:100981800-101010400	Weak transcription	Fetal Thymus	thymus
6	chr9:100983000-101007200	Weak transcription	Fetal Brain Male	brain
7	chr9:100989600-101006400	Weak transcription	Psoas Muscle	Psoas
8	chr9:100989600-101016000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:100991400-101006400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr9:100991400-101010600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr9:100991400-101015400	Weak transcription	Brain Anterior Caudate	brain
12	chr9:100991800-101011400	Weak transcription	Right Ventricle	heart
13	chr9:100992200-101012800	Weak transcription	Brain Substantia Nigra	brain
14	chr9:100992200-101016000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr9:100993200-101010200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr9:100993400-101012600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:100993600-101010400	Weak transcription	Left Ventricle	heart
18	chr9:100995000-101016600	Weak transcription	Brain Angular Gyrus	brain
19	chr9:100995200-101006400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr9:100995200-101010200	Weak transcription	NHDF-Ad	bronchial
21	chr9:100995400-101010400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:100995800-101010400	Weak transcription	Adipose Nuclei	Adipose
23	chr9:100995800-101011200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr9:100996000-101010600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr9:100996000-101010600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr9:100996000-101012400	Weak transcription	Fetal Stomach	stomach
27	chr9:100996000-101016000	Weak transcription	Pancreas	Pancrea
28	chr9:100996200-101017200	Weak transcription	Ovary	ovary
29	chr9:100996600-101010600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr9:100996600-101011200	Weak transcription	Thymus	Thymus
31	chr9:100996800-101006800	Strong transcription	Osteobl	bone
32	chr9:100996800-101011000	Weak transcription	Liver	Liver
33	chr9:100997200-101008800	Weak transcription	Aorta	Aorta
34	chr9:100999600-101008400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr9:101001600-101006600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:101001600-101007000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:101002600-101006600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:101003600-101008800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr9:101003800-101008800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr9:101003800-101010400	Weak transcription	Spleen	Spleen
41	chr9:101003800-101011200	Weak transcription	Gastric	stomach
42	chr9:101004000-101006600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr9:101004000-101010400	Weak transcription	Colonic Mucosa	Colon
44	chr9:101004000-101011000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr9:101004200-101006600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr9:101004200-101010200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr9:101004200-101011000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr9:101004200-101015800	Weak transcription	Brain Hippocampus Middle	brain
49	chr9:101004200-101017200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr9:101004400-101006600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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