Variant report

Variant	rs10818678
Chromosome Location	chr9:101009818-101009819
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100983381..100985865-chr9:101008281..101010298,2	K562	blood:
2	chr9:100987323..100990186-chr9:101009264..101011823,2	K562	blood:
3	chr9:100983664..100985681-chr9:101009334..101011944,2	MCF-7	breast:
4	chr9:101007016..101010479-chr9:101012839..101014596,3	MCF-7	breast:
5	chr9:100954884..100956556-chr9:101008813..101010397,2	K562	blood:

Variant related genes	Relation type
ENSG00000106789	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10115971	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10123643	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10124977	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10760210	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10760216	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760217	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760218	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818627	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818640	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818644	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818645	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818646	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10818648	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10818656	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10818658	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818662	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818666	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818667	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10818668	0.93[ASN][1000 genomes]
rs10818672	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818676	0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs10818677	0.97[ASN][1000 genomes]
rs10818689	0.92[ASN][1000 genomes]
rs10818690	0.92[ASN][1000 genomes]
rs10818691	0.90[ASN][1000 genomes]
rs10818692	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10818693	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10818739	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10818743	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10985517	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10985580	0.93[ASN][1000 genomes]
rs10985583	0.97[ASN][1000 genomes]
rs10985634	0.92[ASN][1000 genomes]
rs10985641	0.89[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs10985642	0.92[CHB][hapmap];1.00[JPT][hapmap];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]
rs10985765	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10985772	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs12237988	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12342612	0.89[ASN][1000 genomes]
rs12346750	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1435253	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1435257	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs1573024	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573025	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17766883	0.80[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17766913	0.80[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1935389	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2900380	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4379551	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742719	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742721	0.85[ASN][1000 genomes]
rs4742722	0.85[ASN][1000 genomes]
rs4743187	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743188	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4743192	0.97[ASN][1000 genomes]
rs4743194	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs5010004	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56262782	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62574277	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62574288	0.85[ASN][1000 genomes]
rs62574300	0.85[ASN][1000 genomes]
rs6478630	0.93[ASN][1000 genomes]
rs6478631	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs67569753	0.93[ASN][1000 genomes]
rs7025781	0.91[ASN][1000 genomes]
rs7032046	0.88[ASN][1000 genomes]
rs7042576	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7045158	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7853442	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7853847	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7859655	0.85[ASN][1000 genomes]
rs7868451	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7873849	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7874856	0.85[ASN][1000 genomes]
rs879368	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879369	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9802650	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10818678	TBC1D2	cis	Thyroid	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

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	chr9:100989600-101016000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:100991400-101010600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr9:100991400-101015400	Weak transcription	Brain Anterior Caudate	brain
9	chr9:100991800-101011400	Weak transcription	Right Ventricle	heart
10	chr9:100992200-101012800	Weak transcription	Brain Substantia Nigra	brain
11	chr9:100992200-101016000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr9:100993200-101010200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr9:100993400-101012600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:100993600-101010400	Weak transcription	Left Ventricle	heart
15	chr9:100995000-101016600	Weak transcription	Brain Angular Gyrus	brain
16	chr9:100995200-101010200	Weak transcription	NHDF-Ad	bronchial
17	chr9:100995400-101010400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:100995800-101010400	Weak transcription	Adipose Nuclei	Adipose
19	chr9:100995800-101011200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr9:100996000-101010600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr9:100996000-101010600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr9:100996000-101012400	Weak transcription	Fetal Stomach	stomach
23	chr9:100996000-101016000	Weak transcription	Pancreas	Pancrea
24	chr9:100996200-101017200	Weak transcription	Ovary	ovary
25	chr9:100996600-101010600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr9:100996600-101011200	Weak transcription	Thymus	Thymus
27	chr9:100996800-101011000	Weak transcription	Liver	Liver
28	chr9:101003800-101010400	Weak transcription	Spleen	Spleen
29	chr9:101003800-101011200	Weak transcription	Gastric	stomach
30	chr9:101004000-101010400	Weak transcription	Colonic Mucosa	Colon
31	chr9:101004000-101011000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr9:101004200-101010200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr9:101004200-101011000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr9:101004200-101015800	Weak transcription	Brain Hippocampus Middle	brain
35	chr9:101004200-101017200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr9:101004400-101010400	Weak transcription	NHLF	lung
37	chr9:101005000-101010400	Weak transcription	Primary T cells from cord blood	blood
38	chr9:101005200-101010600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr9:101005200-101010600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr9:101005200-101017200	Weak transcription	Brain Germinal Matrix	brain
41	chr9:101005800-101010400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:101005800-101010400	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr9:101006000-101010400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr9:101006400-101010200	Weak transcription	NH-A	brain
45	chr9:101006400-101014000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr9:101006600-101010200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr9:101006600-101010200	Weak transcription	Primary B cells from cord blood	blood
48	chr9:101006600-101010200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr9:101006600-101010200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr9:101006600-101010400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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