Variant report

Variant	rs9392669
Chromosome Location	chr6:5294170-5294171
allele	C/T
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	EP300	chr6:5293885-5294210	SK-N-SH_RA	brain:	n/a	chr6:5294010-5294019
2	E2F4	chr6:5294107-5294345	MCF10A-Er-Src	breast:	n/a	n/a
3	MAFK	chr6:5294140-5294340	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5284244..5290564-chr6:5292142..5296092,7	K562	blood:

Variant related genes	Relation type
ENSG00000220446	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1535298	0.86[JPT][hapmap];0.81[AMR][1000 genomes]
rs2326584	0.81[JPT][hapmap]
rs3863215	0.92[ASN][1000 genomes]
rs3863216	0.86[ASN][1000 genomes]
rs6597125	0.81[JPT][hapmap]
rs6908240	0.81[JPT][hapmap]
rs7755157	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9328294	0.81[JPT][hapmap]
rs9378944	1.00[YRI][hapmap]
rs9392668	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9392670	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS 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	10 gene(s)	inside rSNPs	diseases
9	nsv1034463	chr6:5137959-5345678	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
10	nsv1021646	chr6:5157795-5367254	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv538115	chr6:5157795-5367254	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1029609	chr6:5187633-5397254	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv1035080	chr6:5206533-5396019	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv538116	chr6:5206533-5396019	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv1016456	chr6:5216835-5315913	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv538117	chr6:5216835-5315913	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS 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	10 gene(s)	inside rSNPs	diseases
19	nsv1028185	chr6:5247624-5340163	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv830578	chr6:5264086-5455570	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv1022911	chr6:5286297-5322133	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv538119	chr6:5286297-5322133	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9392669	MGC39372	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5262400-5302400	Weak transcription	Aorta	Aorta
2	chr6:5263000-5301000	Weak transcription	Fetal Brain Male	brain
3	chr6:5268000-5294400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:5279400-5298200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:5280800-5308200	Weak transcription	Primary T cells from cord blood	blood
6	chr6:5281000-5294400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr6:5285400-5294600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:5287400-5296200	Weak transcription	Thymus	Thymus
9	chr6:5287800-5294400	Weak transcription	Gastric	stomach
10	chr6:5287800-5313600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:5288000-5294400	Weak transcription	Small Intestine	intestine
12	chr6:5288000-5298200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:5288000-5303000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr6:5288000-5316200	Weak transcription	Fetal Stomach	stomach
15	chr6:5288400-5294400	Weak transcription	Spleen	Spleen
16	chr6:5288400-5294600	Weak transcription	Brain Anterior Caudate	brain
17	chr6:5288400-5294600	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:5288400-5294600	Weak transcription	Left Ventricle	heart
19	chr6:5288400-5294600	Weak transcription	Right Atrium	heart
20	chr6:5288400-5295000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr6:5288400-5295200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:5288400-5302800	Weak transcription	Esophagus	oesophagus
23	chr6:5288400-5324000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:5288400-5331000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:5288600-5294400	Weak transcription	Stomach Mucosa	stomach
26	chr6:5288600-5298200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:5288600-5302800	Weak transcription	HMEC	breast
28	chr6:5288600-5303000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:5288600-5303200	Weak transcription	NHEK	skin
30	chr6:5289000-5294600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr6:5290600-5294400	Weak transcription	GM12878-XiMat	blood
32	chr6:5291200-5298000	Weak transcription	HepG2	liver
33	chr6:5291600-5294200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:5292200-5303200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:5292800-5294600	Weak transcription	Right Ventricle	heart
36	chr6:5292800-5334400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:5293200-5295400	Enhancers	Pancreas	Pancrea
38	chr6:5293400-5295200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:5293400-5295400	Enhancers	Primary hematopoietic stem cells	blood
40	chr6:5293400-5295400	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr6:5293400-5295400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:5293400-5295400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:5293600-5294400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr6:5293600-5301400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr6:5293600-5302200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr6:5293600-5302400	Weak transcription	Colon Smooth Muscle	Colon
47	chr6:5293800-5294600	Weak transcription	Psoas Muscle	Psoas
48	chr6:5293800-5298400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:5293800-5306200	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:5294000-5295000	Enhancers	Fetal Intestine Small	intestine

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