Variant report

Variant	rs7868451
Chromosome Location	chr9:100987622-100987623
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100835130..100837300-chr9:100986077..100988253,2	MCF-7	breast:
2	chr9:100985570..100988965-chr9:100991767..100994360,5	MCF-7	breast:
3	chr9:100987506..100990430-chr9:100991998..100994397,3	K562	blood:
4	chr9:100974489..100979508-chr9:100984246..100988193,5	MCF-7	breast:
5	chr9:100986946..100989189-chr9:101010558..101012631,2	MCF-7	breast:
6	chr9:100978764..100982569-chr9:100985493..100988173,3	K562	blood:
7	chr9:100987427..100990344-chr9:101016703..101018951,2	MCF-7	breast:
8	chr9:100985947..100988574-chr9:101006560..101008071,2	MCF-7	breast:
9	chr9:100987323..100989657-chr9:101010085..101011823,2	K562	blood:
10	chr9:100987323..100990186-chr9:101009264..101011823,2	K562	blood:
11	chr9:100978143..100990074-chr9:101014745..101021064,26	MCF-7	breast:
12	chr9:100968043..100970056-chr9:100986023..100988818,3	MCF-7	breast:
13	chr9:100984926..100990430-chr9:100990519..100995039,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000095380	Chromatin interaction
ENSG00000095383	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10115971	0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10123643	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10124977	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10760210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760216	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10760217	0.91[ASN][1000 genomes]
rs10760218	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10818627	0.91[ASN][1000 genomes]
rs10818640	0.86[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs10818644	0.91[ASN][1000 genomes]
rs10818645	0.91[ASN][1000 genomes]
rs10818646	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10818648	0.89[ASN][1000 genomes]
rs10818656	0.89[ASN][1000 genomes]
rs10818658	0.91[ASN][1000 genomes]
rs10818662	0.90[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs10818666	0.91[ASN][1000 genomes]
rs10818667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10818668	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10818672	0.86[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10818676	0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs10818677	0.89[ASN][1000 genomes]
rs10818678	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10818689	0.84[ASN][1000 genomes]
rs10818690	0.84[ASN][1000 genomes]
rs10818691	0.82[ASN][1000 genomes]
rs10818692	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs10818693	1.00[JPT][hapmap]
rs10818739	1.00[JPT][hapmap]
rs10818743	1.00[JPT][hapmap]
rs10985517	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10985580	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10985583	0.89[ASN][1000 genomes]
rs10985634	0.84[ASN][1000 genomes]
rs10985641	0.85[JPT][hapmap]
rs10985642	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs10985765	1.00[JPT][hapmap]
rs10985772	1.00[JPT][hapmap]
rs12237988	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12342612	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12346750	0.91[ASN][1000 genomes]
rs1435253	1.00[JPT][hapmap]
rs1435257	1.00[JPT][hapmap]
rs1573024	0.91[ASN][1000 genomes]
rs1573025	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17766883	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17766913	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1935389	0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2900380	0.91[ASN][1000 genomes]
rs4379551	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4742719	0.91[ASN][1000 genomes]
rs4743187	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs4743188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4743192	0.89[ASN][1000 genomes]
rs4743194	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5010004	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs62574277	0.89[ASN][1000 genomes]
rs6478630	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478631	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs67569753	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7025781	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7032046	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7042576	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7045158	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7853442	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7853847	1.00[JPT][hapmap]
rs7873849	0.89[ASN][1000 genomes]
rs879368	0.86[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs879369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053729	chr9:100909554-100997718	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
rs7868451	TBC1D2	cis	Thyroid	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100955800-101003200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr9:100961400-101001400	Weak transcription	Right Atrium	heart
3	chr9:100968400-100995600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr9:100968400-100997600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr9:100968600-101010400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr9:100968800-100998000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:100968800-101011000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr9:100969400-101004800	Weak transcription	Brain Germinal Matrix	brain
9	chr9:100969600-100997200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:100969800-100991800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr9:100970200-101001600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr9:100974800-101010600	Weak transcription	Colon Smooth Muscle	Colon
13	chr9:100976400-100998800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:100980200-101010200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr9:100981800-101010400	Weak transcription	Fetal Thymus	thymus
16	chr9:100982200-100990800	Weak transcription	Primary B cells from cord blood	blood
17	chr9:100982200-100991200	Weak transcription	Fetal Lung	lung
18	chr9:100982800-101004600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr9:100983000-100990400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr9:100983000-101007200	Weak transcription	Fetal Brain Male	brain
21	chr9:100983200-100989400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr9:100983200-100990800	Weak transcription	Brain Anterior Caudate	brain
23	chr9:100983200-100992600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:100983200-100996600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr9:100983200-100997600	Weak transcription	Fetal Brain Female	brain
26	chr9:100983400-100987800	Weak transcription	Thymus	Thymus
27	chr9:100983400-100988200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr9:100983400-100990600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr9:100983400-101006200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr9:100983600-100988000	Weak transcription	Brain Hippocampus Middle	brain
31	chr9:100983600-100988800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr9:100983600-100990800	Weak transcription	Right Ventricle	heart
33	chr9:100983600-100994000	Weak transcription	Brain Angular Gyrus	brain
34	chr9:100983800-100988000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr9:100983800-100988600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr9:100983800-100988800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr9:100983800-100989200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr9:100983800-100990600	Weak transcription	Ovary	ovary
39	chr9:100984000-100988400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr9:100984200-100990800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:100984600-100992000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:100984800-100988200	Enhancers	NHDF-Ad	bronchial
43	chr9:100985200-100988600	Enhancers	HepG2	liver
44	chr9:100985400-100988200	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr9:100985600-100987800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr9:100985600-100990400	Genic enhancers	Muscle Satellite Cultured Cells	--
47	chr9:100985600-100998200	Genic enhancers	Fetal Intestine Small	intestine
48	chr9:100985800-100989400	Weak transcription	Left Ventricle	heart
49	chr9:100985800-100990600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr9:100985800-100993200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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