Variant report

Variant	rs750683
Chromosome Location	chr13:30717106-30717107
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:30697642..30699768-chr13:30715433..30718388,2	MCF-7	breast:
2	chr13:30710616..30714136-chr13:30716937..30719066,3	K562	blood:
3	chr13:30716922..30719833-chr13:30752505..30754476,2	MCF-7	breast:
4	chr13:30707361..30710289-chr13:30714464..30717739,4	MCF-7	breast:
5	chr13:30690726..30692990-chr13:30715205..30717386,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2388497	0.80[EUR][1000 genomes]
rs643621	0.80[MEX][hapmap];0.82[TSI][hapmap]
rs656305	0.81[CEU][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7323177	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs913902	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9506267	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040215	chr13:30621351-30741022	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv541745	chr13:30621351-30741022	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv832572	chr13:30650005-30835256	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv981	chr13:30703159-30739838	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv1847946	chr13:30707385-30731192	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs750683	BRCA2	cis	cerebellum	SCAN
rs750683	EEF1DP3	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30700200-30717200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr13:30714400-30718000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:30714600-30717800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr13:30714600-30721800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr13:30715000-30734000	Enhancers	Primary T cells fromperipheralblood	blood
6	chr13:30715200-30717400	Enhancers	Primary B cells from peripheral blood	blood
7	chr13:30715200-30717400	Enhancers	Fetal Thymus	thymus
8	chr13:30715200-30718400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr13:30715200-30727600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr13:30715400-30717200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr13:30715400-30718800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr13:30715400-30720000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr13:30715400-30727200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr13:30715400-30727200	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr13:30715600-30717400	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr13:30715600-30717800	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr13:30715600-30718200	Enhancers	Primary T cells from cord blood	blood
18	chr13:30715600-30719000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr13:30715600-30720000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr13:30715600-30720000	Enhancers	GM12878-XiMat	blood
21	chr13:30715800-30718200	Enhancers	Placenta	Placenta
22	chr13:30715800-30718400	Enhancers	Adipose Nuclei	Adipose
23	chr13:30715800-30718400	Enhancers	NHDF-Ad	bronchial
24	chr13:30716000-30717200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr13:30716000-30717600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr13:30716000-30717600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr13:30716000-30717600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr13:30716000-30717600	Enhancers	NHLF	lung
29	chr13:30716000-30717800	Enhancers	Colon Smooth Muscle	Colon
30	chr13:30716000-30718000	Enhancers	Fetal Muscle Leg	muscle
31	chr13:30716000-30718200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr13:30716000-30718400	Enhancers	HUVEC	blood vessel
33	chr13:30716000-30718600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr13:30716200-30717200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr13:30716200-30717200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr13:30716200-30717400	Enhancers	NH-A	brain
37	chr13:30716200-30717600	Enhancers	Fetal Muscle Trunk	muscle
38	chr13:30716200-30718000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr13:30716400-30717400	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr13:30716400-30717600	Enhancers	Ovary	ovary
41	chr13:30716400-30717600	Enhancers	Spleen	Spleen
42	chr13:30716400-30718000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr13:30716400-30718600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr13:30716600-30717200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr13:30716600-30717200	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr13:30716600-30717200	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr13:30716600-30717400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr13:30716600-30717400	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr13:30716600-30717400	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr13:30716600-30717400	Flanking Active TSS	Hela-S3	cervix

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