Variant report

Variant	rs705599
Chromosome Location	chr6:101304829-101304830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:101302214..101305047-chr6:101327915..101330416,2	MCF-7	breast:
2	chr6:101302750..101305984-chr6:101307403..101310104,4	K562	blood:
3	chr6:101299454..101302050-chr6:101304670..101307311,3	MCF-7	breast:
4	chr6:101302750..101305645-chr6:101307403..101308925,2	K562	blood:

Variant related genes	Relation type
ENSG00000260000	Chromatin interaction
ENSG00000112249	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1069049	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1099911	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11155720	0.81[EUR][1000 genomes]
rs12174782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12530388	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs1754397	0.84[EUR][1000 genomes]
rs1754398	0.84[EUR][1000 genomes]
rs1765058	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2771419	0.84[EUR][1000 genomes]
rs34445308	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4270794	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4454144	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4840159	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs592436	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs593129	0.84[EUR][1000 genomes]
rs618919	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs622353	0.81[EUR][1000 genomes]
rs638823	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs638884	0.83[EUR][1000 genomes]
rs6570972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6570975	0.85[EUR][1000 genomes]
rs6570976	0.85[EUR][1000 genomes]
rs657915	0.91[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs661142	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs664245	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs669716	0.83[EUR][1000 genomes]
rs6919745	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6931410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934256	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs705589	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs705591	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs705592	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs705593	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705600	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705603	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705604	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs705606	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs705607	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs705608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs705610	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs705623	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7738575	0.84[EUR][1000 genomes]
rs7739574	0.91[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7750098	0.80[CEU][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs7750122	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7763793	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7771570	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs817675	0.84[EUR][1000 genomes]
rs846771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846775	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846777	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs846781	0.90[CEU][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs846782	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs846785	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs846794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846797	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs846798	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs863658	0.82[EUR][1000 genomes]
rs865318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9377239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9377242	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9498419	0.87[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1020692	chr6:101136992-101426071	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886457	chr6:101158950-101487473	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1019213	chr6:101225650-101623140	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv538391	chr6:101225650-101623140	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers 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	8 gene(s)	inside rSNPs	diseases
8	esv2763587	chr6:101277874-101510491	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101215200-101311400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:101233600-101306600	Weak transcription	K562	blood
3	chr6:101269200-101326600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:101275800-101314400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:101278000-101306600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:101278000-101313800	Weak transcription	Fetal Intestine Small	intestine
7	chr6:101281200-101317000	Weak transcription	Small Intestine	intestine
8	chr6:101282000-101311400	Weak transcription	Aorta	Aorta
9	chr6:101285600-101326600	Weak transcription	NHLF	lung
10	chr6:101287800-101313000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr6:101290200-101306600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr6:101290200-101318200	Weak transcription	Fetal Lung	lung
13	chr6:101290600-101312800	Weak transcription	Fetal Brain Male	brain
14	chr6:101290800-101311400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:101290800-101311600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:101291200-101326400	Weak transcription	Brain Anterior Caudate	brain
17	chr6:101291400-101314000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:101291600-101314000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr6:101291800-101312800	Weak transcription	Gastric	stomach
20	chr6:101292600-101310800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr6:101294000-101320400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:101294200-101314200	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:101294600-101307000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:101294600-101310800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:101294600-101311400	Weak transcription	Pancreas	Pancrea
26	chr6:101294600-101314400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr6:101294600-101320600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:101294600-101325400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr6:101294600-101328600	Weak transcription	Spleen	Spleen
30	chr6:101294800-101325600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:101295000-101325800	Weak transcription	Brain Angular Gyrus	brain
32	chr6:101295000-101325800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr6:101295800-101305000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:101296000-101323400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr6:101296200-101306800	Weak transcription	HUVEC	blood vessel
36	chr6:101296600-101306800	Weak transcription	HepG2	liver
37	chr6:101296600-101310000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr6:101296800-101307200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr6:101296800-101308400	Weak transcription	Adipose Nuclei	Adipose
40	chr6:101296800-101310200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:101296800-101317000	Weak transcription	HSMMtube	muscle
42	chr6:101296800-101323800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:101297000-101306600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr6:101297000-101306600	Weak transcription	Fetal Intestine Large	intestine
45	chr6:101297000-101310800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr6:101297000-101310800	Weak transcription	Fetal Thymus	thymus
47	chr6:101297000-101311400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr6:101297000-101311400	Weak transcription	Left Ventricle	heart
49	chr6:101297000-101327200	Weak transcription	Fetal Muscle Leg	muscle
50	chr6:101297000-101328200	Weak transcription	Ovary	ovary

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