Variant report

Variant	rs3212646
Chromosome Location	chr5:52386055-52386056
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	NR2F2	chr5:52385936-52386604	MCF-7	breast:	n/a	n/a
2	TCF12	chr5:52385896-52386558	MCF-7	breast:	n/a	n/a
3	MAX	chr5:52386000-52386408	MCF-7	breast:	n/a	n/a
4	EP300	chr5:52385933-52386606	MCF-7	breast:	n/a	chr5:52386001-52386015 chr5:52385996-52386010
5	HDAC2	chr5:52386008-52386553	MCF-7	breast:	n/a	n/a
6	GATA3	chr5:52384958-52386571	MCF-7	breast:	n/a	chr5:52385496-52385504
7	TCF12	chr5:52384953-52386817	MCF-7	breast:	n/a	n/a
8	NR2F2	chr5:52385970-52386530	MCF-7	breast:	n/a	n/a
9	TCF7L2	chr5:52386046-52386596	MCF-7	breast:	n/a	n/a
10	GATA3	chr5:52384907-52386671	MCF-7	breast:	n/a	chr5:52385496-52385504
11	GATA3	chr5:52384627-52386125	SK-N-SH	brain:	n/a	chr5:52385496-52385504
12	GATA3	chr5:52385080-52386527	MCF-7	breast:	n/a	chr5:52385496-52385504
13	ESR1	chr5:52386035-52386357	T-47D	breast:	n/a	n/a
14	POLR2A	chr5:52385987-52386333	SK-N-SH	brain:	n/a	n/a
15	SIN3AK20	chr5:52386026-52386586	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:52384729..52387843-chr5:52404184..52407459,4	MCF-7	breast:
2	chr5:52282372..52286768-chr5:52384365..52386788,6	MCF-7	breast:
3	chr5:52385620..52387718-chr5:52408236..52410843,2	MCF-7	breast:
4	chr5:52246465..52248425-chr5:52385773..52388530,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272123	TF binding region
ENSG00000164171	Chromatin interaction
ENSG00000249899	Chromatin interaction
ENSG00000164172	Chromatin interaction
ENSG00000247796	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs3212431	1.00[YRI][hapmap]
rs3212435	1.00[YRI][hapmap]
rs73756623	0.86[AFR][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	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:52341200-52396400	Strong transcription	HMEC	breast
5	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:52343400-52392800	Weak transcription	Left Ventricle	heart
7	chr5:52346200-52386800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr5:52347600-52387000	Weak transcription	Fetal Stomach	stomach
9	chr5:52347800-52395000	Weak transcription	Psoas Muscle	Psoas
10	chr5:52348600-52394800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:52352400-52389800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:52356800-52394000	Weak transcription	Fetal Kidney	kidney
13	chr5:52360200-52388800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:52361200-52392800	Weak transcription	Small Intestine	intestine
15	chr5:52362200-52387800	Strong transcription	HepG2	liver
16	chr5:52365800-52394800	Weak transcription	Right Ventricle	heart
17	chr5:52367400-52386200	Strong transcription	HUVEC	blood vessel
18	chr5:52367400-52388000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:52368000-52386200	Weak transcription	Aorta	Aorta
20	chr5:52369000-52392800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:52370400-52394600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr5:52370400-52404600	Weak transcription	Brain Germinal Matrix	brain
23	chr5:52372000-52394800	Weak transcription	Colonic Mucosa	Colon
24	chr5:52372000-52394800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr5:52372200-52392800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:52372200-52394800	Weak transcription	Gastric	stomach
27	chr5:52372200-52394800	Weak transcription	Pancreas	Pancrea
28	chr5:52372400-52404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr5:52372800-52386400	Weak transcription	NHDF-Ad	bronchial
30	chr5:52373000-52387000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr5:52373800-52386200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr5:52374200-52392800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:52378400-52405000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:52379200-52388400	Strong transcription	Hela-S3	cervix
35	chr5:52380000-52391200	Weak transcription	Fetal Brain Female	brain
36	chr5:52381000-52386200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr5:52381200-52386200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr5:52381200-52394200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr5:52381800-52386400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:52382800-52395000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr5:52383000-52390800	Weak transcription	Fetal Heart	heart
42	chr5:52383000-52393000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr5:52383000-52394800	Weak transcription	Brain Anterior Caudate	brain
44	chr5:52383200-52394800	Weak transcription	Esophagus	oesophagus
45	chr5:52383200-52394800	Weak transcription	Spleen	Spleen
46	chr5:52383800-52387000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:52383800-52389000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr5:52383800-52392200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr5:52383800-52392800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:52383800-52395000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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