Variant report

Variant	rs71325390
Chromosome Location	chr3:119356440-119356441
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	POLR2A	chr3:119356412-119358188	GM12892	blood:	n/a	n/a
2	ATF2	chr3:119356350-119357387	GM12878	blood:	n/a	n/a
3	GATA3	chr3:119356390-119359464	SK-N-SH	brain:	n/a	chr3:119357125-119357135 chr3:119357061-119357071
4	NFIC	chr3:119356328-119359285	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:119356431-119357388	U87	brain:	n/a	n/a
6	EP300	chr3:119355708-119359660	SK-N-SH	brain:	n/a	chr3:119358021-119358035 chr3:119358549-119358558 chr3:119357930-119357938 chr3:119356957-119356971 chr3:119356958-119356972
7	TCF12	chr3:119356436-119358312	SK-N-SH	brain:	n/a	chr3:119357774-119357782
8	TCF12	chr3:119356402-119359447	SK-N-SH	brain:	n/a	chr3:119357774-119357782
9	GATA1	chr3:119356391-119357306	K562	blood:	n/a	chr3:119357125-119357135 chr3:119357061-119357071
10	GATA2	chr3:119356439-119357261	SH-SY5Y	brain:	n/a	chr3:119357125-119357135 chr3:119357061-119357071
11	POLR2A	chr3:119356420-119358219	GM12892	blood:	n/a	n/a
12	POLR2A	chr3:119356423-119358169	GM12891	blood:	n/a	n/a
13	POLR2A	chr3:119356403-119358211	GM12891	blood:	n/a	n/a
14	MTA3	chr3:119356439-119358832	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:119356373-119358587	GM12878	blood:	n/a	n/a
16	PML	chr3:119356256-119359119	GM12878	blood:	n/a	n/a
17	RUNX3	chr3:119356354-119358964	GM12878	blood:	n/a	n/a
18	JUND	chr3:119356288-119359356	SK-N-SH	brain:	n/a	chr3:119358550-119358558 chr3:119358549-119358558 chr3:119358575-119358587 chr3:119358551-119358558
19	POLR2A	chr3:119356371-119358220	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:119356320-119357388	U87	brain:	n/a	n/a
21	EP300	chr3:119356419-119357518	SK-N-SH	brain:	n/a	chr3:119356957-119356971 chr3:119356958-119356972
22	JUN	chr3:119356390-119357329	K562	blood:	n/a	n/a
23	NFIC	chr3:119356385-119358183	SK-N-SH	brain:	n/a	n/a
24	MTA3	chr3:119356363-119358756	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:119355104..119356665-chr3:119359282..119361780,2	K562	blood:
2	chr3:119344313..119346275-chr3:119356031..119358042,2	K562	blood:
3	chr3:119180931..119183365-chr3:119356123..119357901,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242052	TF binding region
ENSG00000121577	Chromatin interaction
ENSG00000176142	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12023	0.81[AFR][1000 genomes]
rs13062697	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095802	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13323756	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293235	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2319013	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786295	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6792223	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794067	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835803	0.97[ASN][1000 genomes]
rs9837943	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865825	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873256	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers 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	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv1796433	chr3:119350324-119360506	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv1804126	chr3:119351398-119360506	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv527724	chr3:119353844-119361415	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv963275	chr3:119355854-119358012	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119340800-119357600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:119341400-119364600	Weak transcription	Liver	Liver
3	chr3:119345200-119357600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:119349400-119357600	Weak transcription	Fetal Intestine Small	intestine
5	chr3:119349600-119357000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr3:119349800-119357000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:119349800-119378800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:119352000-119357400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:119352000-119378600	Weak transcription	Thymus	Thymus
10	chr3:119352600-119367000	Weak transcription	Ovary	ovary
11	chr3:119352800-119356600	Weak transcription	Aorta	Aorta
12	chr3:119353800-119359000	Strong transcription	Stomach Smooth Muscle	stomach
13	chr3:119354000-119356600	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr3:119354000-119358000	Enhancers	Fetal Heart	heart
15	chr3:119354000-119358600	Enhancers	Left Ventricle	heart
16	chr3:119354000-119358800	Enhancers	Placenta	Placenta
17	chr3:119354000-119387600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:119354400-119358400	Enhancers	Adipose Nuclei	Adipose
19	chr3:119354400-119358400	Enhancers	Right Atrium	heart
20	chr3:119354400-119358800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr3:119354600-119356600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr3:119354600-119356600	Enhancers	GM12878-XiMat	blood
23	chr3:119354600-119357800	Enhancers	Psoas Muscle	Psoas
24	chr3:119354600-119358400	Enhancers	HUVEC	blood vessel
25	chr3:119354800-119356600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:119354800-119356600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:119354800-119356600	Enhancers	NHDF-Ad	bronchial
28	chr3:119354800-119358400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:119354800-119358400	Enhancers	HSMM	muscle
30	chr3:119354800-119358600	Enhancers	Small Intestine	intestine
31	chr3:119354800-119358600	Enhancers	HMEC	breast
32	chr3:119354800-119360400	Weak transcription	Lung	lung
33	chr3:119355000-119356600	Enhancers	Primary hematopoietic stem cells	blood
34	chr3:119355000-119356600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr3:119355000-119356600	Enhancers	Osteobl	bone
36	chr3:119355000-119356800	Enhancers	Stomach Mucosa	stomach
37	chr3:119355000-119357000	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr3:119355000-119357000	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr3:119355000-119357600	Weak transcription	Esophagus	oesophagus
40	chr3:119355000-119357600	Weak transcription	Fetal Stomach	stomach
41	chr3:119355000-119358000	Enhancers	Spleen	Spleen
42	chr3:119355000-119358200	Enhancers	HSMMtube	muscle
43	chr3:119355000-119358200	Enhancers	NHLF	lung
44	chr3:119355000-119358400	Enhancers	K562	blood
45	chr3:119355200-119358200	Enhancers	Placenta Amnion	Placenta Amnion
46	chr3:119355400-119356600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:119355400-119356600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:119355400-119358600	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr3:119355400-119361000	Weak transcription	Pancreas	Pancrea
50	chr3:119355600-119357000	Enhancers	Right Ventricle	heart

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