Variant report

Variant	rs9458825
Chromosome Location	chr6:163845192-163845193
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:163844458-163845666	K562	blood:	n/a	n/a
2	GATA3	chr6:163844617-163845336	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr6:163844730-163845232	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr6:163844841-163845209	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:163844662..163847045-chr6:163859401..163861276,2	MCF-7	breast:
2	chr6:163837219..163840006-chr6:163844641..163847487,2	K562	blood:
3	chr6:163842546..163846148-chr6:163847006..163850145,4	K562	blood:

Variant related genes	Relation type
QKI	TF binding region
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10080505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12523713	0.92[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12523978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17176494	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4112651	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60332904	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6455905	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs6901592	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6902608	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6906081	0.90[EUR][1000 genomes]
rs6906275	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6906725	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6910323	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6914093	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6917030	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6928869	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6936927	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6937072	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6937097	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73013516	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73013528	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73013553	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73015316	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7748261	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7759606	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7761090	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7770852	0.92[CEU][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9456868	0.91[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9458821	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9458823	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458827	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458828	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458830	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9458837	0.92[CEU][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9458849	0.92[CEU][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9458857	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9458859	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs9654569	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1797109	chr6:163834147-163908115	Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1019551	chr6:163842358-163965216	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163837400-163857200	Weak transcription	Spleen	Spleen
2	chr6:163837800-163851000	Weak transcription	Small Intestine	intestine
3	chr6:163838000-163847600	Weak transcription	Pancreas	Pancrea
4	chr6:163838000-163851600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:163838000-163860600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr6:163838800-163845200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:163839200-163845400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr6:163839600-163846200	Weak transcription	Thymus	Thymus
9	chr6:163839800-163851600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr6:163840800-163865000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr6:163840800-163881400	Weak transcription	Fetal Stomach	stomach
12	chr6:163841000-163847600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr6:163841600-163845800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr6:163841600-163847400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:163841600-163847400	Weak transcription	Aorta	Aorta
16	chr6:163841600-163848000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:163841600-163848600	Weak transcription	HMEC	breast
18	chr6:163841600-163853200	Enhancers	Adipose Nuclei	Adipose
19	chr6:163841600-163858600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:163841600-163864400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:163841800-163845600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:163841800-163848600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:163841800-163851000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:163842000-163845200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:163842000-163846000	Weak transcription	Stomach Mucosa	stomach
26	chr6:163842000-163847600	Enhancers	Fetal Brain Male	brain
27	chr6:163842000-163848200	Weak transcription	GM12878-XiMat	blood
28	chr6:163842000-163850000	Weak transcription	HSMMtube	muscle
29	chr6:163842200-163851000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr6:163842400-163847200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr6:163842400-163848000	Weak transcription	Fetal Lung	lung
32	chr6:163842400-163849800	Weak transcription	Primary T cells from cord blood	blood
33	chr6:163842600-163845400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr6:163842600-163847400	Weak transcription	HUVEC	blood vessel
35	chr6:163842600-163865200	Weak transcription	Fetal Kidney	kidney
36	chr6:163842800-163846400	Enhancers	Ovary	ovary
37	chr6:163843000-163845600	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr6:163843000-163845800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr6:163843000-163846600	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr6:163843200-163845400	Genic enhancers	Fetal Muscle Leg	muscle
41	chr6:163843200-163848600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr6:163843400-163845200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr6:163843400-163845200	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:163843400-163845800	Enhancers	NH-A	brain
45	chr6:163843400-163846400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:163843400-163846400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:163843400-163846400	Enhancers	Psoas Muscle	Psoas
48	chr6:163843600-163845200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:163843600-163845200	Enhancers	Stomach Smooth Muscle	stomach
50	chr6:163843600-163845600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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