Variant report

Variant	rs901380
Chromosome Location	chr5:177029407-177029408
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	chr5:177028714-177029850	K562	blood:	n/a	n/a
2	GATA3	chr5:177029242-177029519	T-47D	breast:	n/a	chr5:177029426-177029436 chr5:177029428-177029435 chr5:177029427-177029435 chr5:177029417-177029434 chr5:177029428-177029435 chr5:177029426-177029435 chr5:177029428-177029435
3	POLR2A	chr5:177029361-177029734	GM12878	blood:	n/a	n/a
4	GATA3	chr5:177029185-177029533	MCF-7	breast:	n/a	chr5:177029426-177029436 chr5:177029428-177029435 chr5:177029427-177029435 chr5:177029417-177029434 chr5:177029428-177029435 chr5:177029426-177029435 chr5:177029428-177029435
5	POLR2A	chr5:177029097-177029524	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr5:177029344-177029824	GM12878	blood:	n/a	n/a
7	POLR2A	chr5:177028523-177029699	HepG2	liver:	n/a	n/a
8	POLR2A	chr5:177028515-177029414	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr5:177029337-177029777	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:176979030..176982090-chr5:177027612..177030348,3	K562	blood:
2	chr5:177028879..177031069-chr5:177037476..177041584,3	MCF-7	breast:
3	chr5:176935179..176936864-chr5:177027186..177030051,3	K562	blood:
4	chr5:176923028..176926285-chr5:177025596..177029619,3	MCF-7	breast:
5	chr5:176979154..176982725-chr5:177026070..177029438,5	MCF-7	breast:

Variant related genes	Relation type
B4GALT7	TF binding region
ENSG00000272459	Chromatin interaction
ENSG00000247679	Chromatin interaction
ENSG00000146094	Chromatin interaction
ENSG00000146067	Chromatin interaction
ENSG00000196923	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs28499092	0.84[EUR][1000 genomes]
rs28595585	0.97[EUR][1000 genomes]
rs55646352	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55869062	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55975666	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56190755	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56664111	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57593509	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57960711	0.94[EUR][1000 genomes]
rs59621415	0.94[EUR][1000 genomes]
rs59666704	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60634107	0.94[EUR][1000 genomes]
rs61334447	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73337744	0.94[EUR][1000 genomes]
rs73337753	0.94[EUR][1000 genomes]
rs73337757	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73337765	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73337767	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73337782	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73337783	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73337790	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73339755	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73339759	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7735142	1.00[CEU][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	nsv916108	chr5:176688459-177078723	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
2	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
3	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer 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	78 gene(s)	inside rSNPs	diseases
4	nsv883181	chr5:176978496-177034786	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv883182	chr5:176980995-177322056	Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv883183	chr5:177019379-177030351	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177028000-177029600	Enhancers	Gastric	stomach
2	chr5:177028000-177029800	Enhancers	Esophagus	oesophagus
3	chr5:177028000-177030600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:177028000-177032200	Weak transcription	Aorta	Aorta
5	chr5:177028000-177034200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:177028000-177034200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:177028000-177040000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:177028200-177029600	Enhancers	Brain Cingulate Gyrus	brain
9	chr5:177028200-177029800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr5:177028200-177029800	Enhancers	Adipose Nuclei	Adipose
11	chr5:177028200-177029800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr5:177028200-177031400	Weak transcription	Thymus	Thymus
13	chr5:177028200-177033600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:177028200-177034200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr5:177028200-177034400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr5:177028200-177035600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr5:177028200-177036400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr5:177028200-177038000	Weak transcription	Right Atrium	heart
19	chr5:177028400-177029800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr5:177028400-177029800	Enhancers	Pancreas	Pancrea
21	chr5:177028400-177030000	Enhancers	Brain Hippocampus Middle	brain
22	chr5:177028400-177030000	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr5:177028400-177030200	Weak transcription	Placenta	Placenta
24	chr5:177028400-177030200	Weak transcription	HSMMtube	muscle
25	chr5:177028400-177030400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr5:177028400-177030400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr5:177028400-177030600	Weak transcription	Spleen	Spleen
28	chr5:177028400-177030800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:177028400-177031200	Weak transcription	Colonic Mucosa	Colon
30	chr5:177028400-177031600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:177028400-177031800	Weak transcription	Primary T cells from cord blood	blood
32	chr5:177028400-177031800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr5:177028400-177032000	Weak transcription	Lung	lung
34	chr5:177028400-177032000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr5:177028400-177032200	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr5:177028400-177034000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr5:177028400-177034000	Weak transcription	A549	lung
38	chr5:177028400-177034200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr5:177028400-177034200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr5:177028400-177034800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr5:177028400-177036600	Weak transcription	HMEC	breast
42	chr5:177028400-177040200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr5:177028400-177042600	Weak transcription	Primary B cells from cord blood	blood
44	chr5:177028400-177044800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr5:177028400-177045800	Weak transcription	Left Ventricle	heart
46	chr5:177028400-177045800	Weak transcription	Psoas Muscle	Psoas
47	chr5:177028400-177048400	Weak transcription	NH-A	brain
48	chr5:177028600-177030600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr5:177028600-177030800	Weak transcription	Fetal Intestine Large	intestine
50	chr5:177028600-177031200	Weak transcription	Brain Germinal Matrix	brain

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