Variant report

Variant	rs6787569
Chromosome Location	chr3:69132554-69132555
allele	A/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	RELA	chr3:69131918-69132578	GM15510	blood:	n/a	chr3:69132178-69132187 chr3:69132178-69132187
2	PML	chr3:69131714-69132557	GM12878	blood:	n/a	chr3:69131737-69131746 chr3:69131734-69131743 chr3:69131880-69131888
3	NFIC	chr3:69131523-69132588	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:69128206-69135962	GM12878	blood:	n/a	n/a
5	EBF1	chr3:69131435-69132761	GM12878	blood:	n/a	chr3:69132172-69132183
6	TBL1XR1	chr3:69131847-69132597	GM12878	blood:	n/a	n/a
7	STAT1	chr3:69131939-69132849	Hela-S3	cervix:	n/a	chr3:69132200-69132207
8	STAT3	chr3:69131167-69132613	MCF10A-Er-Src	breast:	n/a	chr3:69131735-69131744 chr3:69132200-69132207 chr3:69131661-69131673 chr3:69131736-69131745
9	STAT3	chr3:69131196-69132575	MCF10A-Er-Src	breast:	n/a	chr3:69131735-69131744 chr3:69132200-69132207 chr3:69131661-69131673 chr3:69131736-69131745
10	MTA3	chr3:69131863-69132594	GM12878	blood:	n/a	n/a
11	KAP1	chr3:69131884-69132570	U2OS	brain:	n/a	n/a
12	STAT3	chr3:69131779-69132559	GM12878	blood:	n/a	chr3:69132200-69132207
13	RCOR1	chr3:69131783-69132595	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:69131870-69132554	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:69130649-69132842	GM12891	blood:	n/a	n/a
16	RELA	chr3:69131849-69132628	GM12878	blood:	n/a	chr3:69132178-69132187 chr3:69132178-69132187
17	RELA	chr3:69131980-69132675	GM18526	blood:	n/a	chr3:69132178-69132187 chr3:69132178-69132187

No.	Distal block	Cell Line	Cell type
1	chr3:69099731..69103494-chr3:69131306..69136379,6	MCF-7	breast:
2	chr3:69061476..69064768-chr3:69131300..69135318,3	K562	blood:
3	chr3:69128084..69131909-chr3:69132505..69136999,7	K562	blood:
4	chr3:69127777..69131218-chr3:69132524..69136559,5	K562	blood:
5	chr3:69061713..69064386-chr3:69131300..69133862,4	K562	blood:

Variant related genes	Relation type
ARL6IP5	TF binding region
UBA3	TF binding region
ENSG00000163378	Chromatin interaction
ENSG00000144744	Chromatin interaction
ENSG00000144747	Chromatin interaction
ENSG00000244513	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs2009602	0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2271122	0.86[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap];0.84[MKK][hapmap]
rs2292198	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35718539	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3755717	0.84[AFR][1000 genomes]
rs3755721	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772979	0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3821562	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3853157	0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.85[MKK][hapmap];0.80[ASN][1000 genomes]
rs56156415	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs58950441	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6549181	0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs6549184	1.00[MEX][hapmap]
rs6775065	0.81[ASN][1000 genomes]
rs6775256	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]
rs6777032	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs6782474	0.83[MKK][hapmap]
rs714300	0.81[ASN][1000 genomes]
rs7615341	0.81[ASN][1000 genomes]
rs9813514	0.93[CHB][hapmap];0.81[JPT][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876933	chr3:69059023-69227379	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv876934	chr3:69111512-69166895	Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69129400-69133400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:69129400-69133400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:69129400-69134000	Weak transcription	Gastric	stomach
4	chr3:69129600-69133200	Enhancers	Hela-S3	cervix
5	chr3:69129600-69133400	Weak transcription	Esophagus	oesophagus
6	chr3:69129600-69133400	Weak transcription	Pancreas	Pancrea
7	chr3:69129600-69133600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:69129600-69133600	Weak transcription	Right Ventricle	heart
9	chr3:69129600-69134000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:69129600-69134000	Enhancers	Small Intestine	intestine
11	chr3:69129800-69133200	Enhancers	Fetal Heart	heart
12	chr3:69129800-69133200	Enhancers	HMEC	breast
13	chr3:69129800-69133400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:69129800-69133400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr3:69129800-69133400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:69130000-69132600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:69130000-69132800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr3:69130000-69133000	Weak transcription	Liver	Liver
19	chr3:69130000-69133200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:69130000-69133200	Weak transcription	Colonic Mucosa	Colon
21	chr3:69130000-69133200	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr3:69130000-69133200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:69130000-69133200	Enhancers	HUVEC	blood vessel
24	chr3:69130000-69133400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:69130000-69133400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:69130000-69133400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:69130000-69133400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:69130000-69133400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr3:69130000-69133400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:69130000-69133400	Enhancers	Brain Angular Gyrus	brain
31	chr3:69130000-69133400	Weak transcription	Brain Germinal Matrix	brain
32	chr3:69130000-69133400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:69130000-69133400	Enhancers	Brain Substantia Nigra	brain
34	chr3:69130000-69133400	Enhancers	Fetal Intestine Small	intestine
35	chr3:69130000-69133400	Weak transcription	Fetal Kidney	kidney
36	chr3:69130000-69133400	Weak transcription	Fetal Stomach	stomach
37	chr3:69130000-69133400	Enhancers	K562	blood
38	chr3:69130000-69133600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:69130000-69133600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr3:69130000-69133600	Enhancers	Primary T cells fromperipheralblood	blood
41	chr3:69130000-69133600	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr3:69130000-69133600	Weak transcription	Aorta	Aorta
43	chr3:69130000-69133600	Enhancers	Fetal Intestine Large	intestine
44	chr3:69130000-69133600	Weak transcription	Fetal Muscle Trunk	muscle
45	chr3:69130200-69132800	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:69130200-69133200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:69130200-69133400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:69130200-69133400	Weak transcription	Fetal Brain Female	brain
49	chr3:69130400-69132800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr3:69130400-69133200	Enhancers	Duodenum Mucosa	Duodenum

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