Variant report

Variant	rs1053506
Chromosome Location	chr15:78287476-78287477
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78259091..78259732-chr15:78286600..78287504,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH2D7-3	chr15:78287362-78287631	ENSG00000259792.1

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10775214	1.00[YRI][hapmap]
rs10775215	1.00[ASN][1000 genomes]
rs11072725	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11072726	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11633329	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11633569	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11636889	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11854102	0.84[AMR][1000 genomes]
rs12595595	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12898535	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12900731	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12901492	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12913206	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12915731	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs12915847	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12916320	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1348256	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16969502	1.00[CEU][hapmap]
rs17477813	0.84[YRI][hapmap]
rs1837911	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1837912	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2015951	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2044100	0.89[AFR][1000 genomes]
rs2867984	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28680277	1.00[ASN][1000 genomes]
rs3972617	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4243072	1.00[ASN][1000 genomes]
rs4316722	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4411474	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4886551	1.00[ASN][1000 genomes]
rs4886552	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4886556	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4886985	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4886986	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4886987	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4886990	1.00[ASN][1000 genomes]
rs4886991	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4886993	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4886997	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4886998	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4887001	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4887002	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4887003	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4887004	1.00[ASN][1000 genomes]
rs4997420	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs61732053	1.00[ASN][1000 genomes]
rs7163997	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7169882	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7170101	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7170286	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7170452	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7174640	1.00[CEU][hapmap]
rs7175192	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7175235	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7175975	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7180684	1.00[JPT][hapmap]
rs8025423	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8033216	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs894295	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs894296	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs894302	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9788640	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9920180	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 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	chr15:78278400-78288800	Enhancers	Fetal Muscle Leg	muscle
2	chr15:78279400-78287600	Enhancers	Fetal Heart	heart
3	chr15:78279400-78287800	Enhancers	Adipose Nuclei	Adipose
4	chr15:78279400-78289800	Enhancers	Ovary	ovary
5	chr15:78279800-78289600	Weak transcription	Fetal Brain Female	brain
6	chr15:78280000-78290400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr15:78280200-78295800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:78280800-78287600	Enhancers	Right Ventricle	heart
9	chr15:78281000-78289600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:78281800-78287600	Enhancers	Right Atrium	heart
11	chr15:78282000-78287800	Enhancers	Rectal Smooth Muscle	rectum
12	chr15:78282200-78287600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:78282200-78287800	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr15:78282200-78289600	Enhancers	NHLF	lung
15	chr15:78282400-78288800	Enhancers	HMEC	breast
16	chr15:78282600-78287800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:78282600-78287800	Enhancers	Brain Substantia Nigra	brain
18	chr15:78282600-78287800	Enhancers	Colon Smooth Muscle	Colon
19	chr15:78282600-78287800	Enhancers	Stomach Mucosa	stomach
20	chr15:78282600-78288000	Enhancers	HUVEC	blood vessel
21	chr15:78282600-78288200	Enhancers	NHDF-Ad	bronchial
22	chr15:78283400-78289000	Weak transcription	Primary T cells from cord blood	blood
23	chr15:78283400-78290000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr15:78283400-78291200	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr15:78283400-78292800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr15:78283400-78293400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:78283400-78296400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr15:78283400-78305000	Weak transcription	K562	blood
29	chr15:78283600-78288600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr15:78283600-78288600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:78283600-78289800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:78283600-78289800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr15:78283600-78294800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:78283600-78300800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:78283800-78289600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr15:78283800-78290800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr15:78283800-78301000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr15:78284200-78287800	Enhancers	Placenta Amnion	Placenta Amnion
39	chr15:78284200-78290000	Genic enhancers	Fetal Stomach	stomach
40	chr15:78284400-78289800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr15:78284600-78310200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr15:78284800-78289400	Weak transcription	Dnd41	blood
43	chr15:78284800-78296400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:78285000-78288000	Enhancers	Stomach Smooth Muscle	stomach
45	chr15:78285000-78289800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr15:78285000-78289800	Weak transcription	HepG2	liver
47	chr15:78285200-78287600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:78285400-78290000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr15:78285400-78290000	Genic enhancers	Fetal Thymus	thymus
50	chr15:78285400-78295800	Weak transcription	H1 Cell Line	embryonic stem cell

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