Variant report

Variant	rs6459403
Chromosome Location	chr6:15243806-15243807
allele	A/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	USF2	chr6:15243592-15243827	H1-hESC	embryonic stem cell:	n/a	n/a
2	CEBPB	chr6:15243448-15243884	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr6:15243797-15248662	SK-N-SH	brain:	n/a	n/a
4	SIN3A	chr6:15243580-15243984	H1-hESC	embryonic stem cell:	n/a	chr6:15243746-15243755
5	STAT3	chr6:15243663-15243857	MCF10A-Er-Src	breast:	n/a	chr6:15243684-15243696 chr6:15243824-15243835 chr6:15243680-15243688
6	USF1	chr6:15243503-15243971	H1-hESC	embryonic stem cell:	n/a	n/a
7	JUN	chr6:15243656-15243856	H1-hESC	embryonic stem cell:	n/a	n/a
8	JUND	chr6:15243646-15243845	H1-hESC	embryonic stem cell:	n/a	n/a
9	NFYB	chr6:15243645-15243840	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:15226832..15230438-chr6:15243233..15244837,3	K562	blood:
2	chr6:15085986..15094450-chr6:15243173..15249347,32	MCF-7	breast:
3	chr6:15088518..15090840-chr6:15243708..15248817,8	MCF-7	breast:
4	chr6:15239185..15241876-chr6:15241948..15244748,3	MCF-7	breast:
5	chr6:15242226..15244729-chr6:15276839..15280020,3	K562	blood:

Variant related genes	Relation type
JARID2	TF binding region
ENSG00000234261	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10949286	0.83[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10949287	0.88[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10949289	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10949290	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11757859	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11760130	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12196030	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12207467	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55786434	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67032298	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72834541	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs752861	0.88[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830593	chr6:15049636-15244190	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv830594	chr6:15171158-15261296	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15240000-15244400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr6:15240000-15244600	Weak transcription	Left Ventricle	heart
3	chr6:15240000-15244600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:15240000-15244800	Weak transcription	Aorta	Aorta
5	chr6:15240000-15244800	Weak transcription	Right Atrium	heart
6	chr6:15240200-15244600	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:15240400-15244000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:15240400-15244200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:15240400-15244200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:15240400-15244400	Weak transcription	Fetal Brain Female	brain
11	chr6:15240400-15244400	Weak transcription	Fetal Lung	lung
12	chr6:15240400-15244400	Weak transcription	Fetal Stomach	stomach
13	chr6:15240400-15244400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:15240400-15244600	Weak transcription	Brain Substantia Nigra	brain
15	chr6:15240400-15244600	Weak transcription	HSMMtube	muscle
16	chr6:15240600-15244400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:15240600-15244600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:15240600-15244600	Weak transcription	Brain Germinal Matrix	brain
19	chr6:15240600-15244600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:15240600-15244600	Weak transcription	HSMM	muscle
21	chr6:15240600-15244800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:15240800-15244200	Weak transcription	Fetal Heart	heart
23	chr6:15241000-15244600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:15242200-15244000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:15242400-15244000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr6:15242600-15244000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:15242600-15244400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:15242800-15244200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr6:15242800-15244200	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr6:15242800-15244600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr6:15243000-15244200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:15243000-15244600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr6:15243000-15244600	Enhancers	HUVEC	blood vessel
34	chr6:15243000-15244800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr6:15243200-15244200	Enhancers	HepG2	liver
36	chr6:15243200-15244400	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr6:15243200-15244400	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr6:15243200-15244400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:15243200-15244600	Enhancers	Primary B cells from cord blood	blood
40	chr6:15243200-15245400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr6:15243200-15248400	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr6:15243400-15244200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:15243400-15244400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:15243400-15244400	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr6:15243400-15244400	Enhancers	Primary hematopoietic stem cells	blood
46	chr6:15243400-15244400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr6:15243400-15244600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
48	chr6:15243400-15244600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:15243600-15244200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:15243600-15244600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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