Variant report

Variant	rs10005531
Chromosome Location	chr4:78820513-78820514
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78739655..78741254-chr4:78819891..78822561,2	MCF-7	breast:
2	chr4:78819042..78822002-chr4:78825525..78828218,2	K562	blood:
3	chr4:78783060..78785157-chr4:78820001..78822393,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169288	Chromatin interaction
ENSG00000138767	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10005935	0.81[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap]
rs10018117	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10019920	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10026176	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10027634	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10027739	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs10030568	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10049674	1.00[CEU][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1106457	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs11931686	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11942975	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12509847	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13131331	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1587563	0.85[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap]
rs17002804	0.94[ASW][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.93[YRI][hapmap]
rs2036455	0.92[CEU][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs2036457	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs28417234	0.85[EUR][1000 genomes]
rs28436599	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28685099	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4128860	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4328941	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859512	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4859513	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4859882	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859884	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859890	1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6533225	0.80[CEU][hapmap];0.85[CHB][hapmap];0.93[YRI][hapmap]
rs6533355	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6533372	0.84[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs67814821	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6811439	0.81[ASN][1000 genomes]
rs6814088	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6820725	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6835993	0.81[CHB][hapmap];0.93[YRI][hapmap]
rs6849145	0.88[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7436080	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7660788	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7682450	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs873280	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs924684	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs924685	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9654194	0.90[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.81[ASN][1000 genomes]
rs9994366	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv1818157	chr4:78678104-78849088	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv1824966	chr4:78747771-78823070	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv516836	chr4:78748977-78981919	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv594704	chr4:78748977-78981919	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv461562	chr4:78757015-78981919	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv461563	chr4:78757015-78981919	Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv594705	chr4:78757015-78981919	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1008217	chr4:78777531-78957311	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv537145	chr4:78777531-78957311	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10005531	BTC	cis	parietal	SCAN
rs10005531	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78784800-78842200	Weak transcription	HSMMtube	muscle
2	chr4:78784800-78859800	Weak transcription	Esophagus	oesophagus
3	chr4:78785000-78831200	Weak transcription	Brain Angular Gyrus	brain
4	chr4:78785000-78831600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr4:78785000-78841800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:78785000-78874400	Weak transcription	Right Ventricle	heart
7	chr4:78785200-78820800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:78785400-78829800	Weak transcription	Fetal Heart	heart
9	chr4:78790600-78843400	Weak transcription	Small Intestine	intestine
10	chr4:78794000-78851200	Weak transcription	Spleen	Spleen
11	chr4:78794200-78851800	Weak transcription	Lung	lung
12	chr4:78795600-78831800	Weak transcription	NHLF	lung
13	chr4:78795600-78833000	Weak transcription	Brain Germinal Matrix	brain
14	chr4:78799200-78832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:78802400-78858400	Weak transcription	Aorta	Aorta
16	chr4:78806000-78841400	Weak transcription	A549	lung
17	chr4:78806000-78881000	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:78806600-78875600	Weak transcription	Colonic Mucosa	Colon
19	chr4:78808800-78820600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:78808800-78852400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:78809000-78825000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:78809200-78836800	Weak transcription	Fetal Brain Female	brain
23	chr4:78809200-78837400	Weak transcription	Fetal Brain Male	brain
24	chr4:78809200-78847000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr4:78809400-78820600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr4:78809400-78820600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr4:78809400-78824400	Weak transcription	Fetal Kidney	kidney
28	chr4:78809400-78829800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:78809400-78831000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:78809400-78831200	Weak transcription	Brain Substantia Nigra	brain
31	chr4:78809400-78831600	Weak transcription	Brain Anterior Caudate	brain
32	chr4:78809400-78834400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr4:78809400-78841000	Weak transcription	Hela-S3	cervix
34	chr4:78809600-78851200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:78809600-78851400	Weak transcription	Ovary	ovary
36	chr4:78809600-78865400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr4:78809600-78881200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr4:78810000-78829800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:78810000-78851800	Weak transcription	Thymus	Thymus
40	chr4:78810400-78843400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr4:78812800-78823600	Strong transcription	Primary T cells from cord blood	blood
42	chr4:78814000-78825400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr4:78814000-78841600	Weak transcription	Osteobl	bone
44	chr4:78814400-78829600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:78814600-78828600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:78814600-78829000	Weak transcription	Fetal Intestine Large	intestine
47	chr4:78814600-78829800	Weak transcription	Fetal Stomach	stomach
48	chr4:78814600-78829800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr4:78814600-78843400	Weak transcription	Left Ventricle	heart
50	chr4:78814600-78874400	Weak transcription	Pancreas	Pancrea

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