Variant report

Variant	rs8042600
Chromosome Location	chr15:100241957-100241958
allele	A/C
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	NFATC1	chr15:100240548-100242407	GM12878	blood:	n/a	chr15:100242190-100242203
2	POLR2A	chr15:100241895-100242770	GM12892	blood:	n/a	n/a
3	POLR2A	chr15:100241319-100242042	GM12891	blood:	n/a	n/a
4	STAT5A	chr15:100240468-100242456	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:100240565-100242556	GM12878	blood:	n/a	n/a
6	POLR2A	chr15:100240550-100242551	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:100104091..100109623-chr15:100241901..100248412,10	MCF-7	breast:

Variant related genes	Relation type
MEF2A	TF binding region
ENSG00000068305	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12101528	1.00[CEU][hapmap]
rs13329194	1.00[CEU][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs182730	1.00[CEU][hapmap]
rs2570803	1.00[CEU][hapmap]
rs2570824	1.00[CEU][hapmap]
rs2570931	1.00[CEU][hapmap]
rs2570932	1.00[CEU][hapmap]
rs2570933	1.00[CEU][hapmap]
rs28497795	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28520235	0.85[AMR][1000 genomes]
rs28838709	0.82[AFR][1000 genomes]
rs8029516	1.00[CEU][hapmap]
rs8032302	1.00[CEU][hapmap]
rs8039892	1.00[CEU][hapmap];0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1038005	chr15:100170414-100633714	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv542522	chr15:100170414-100633714	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv904559	chr15:100174907-100255046	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv904560	chr15:100196657-100339331	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv904561	chr15:100204918-100486828	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv428313	chr15:100236203-100757039	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv904563	chr15:100239546-100274747	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
11	nsv570730	chr15:100240910-100700520	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100159000-100253000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:100171200-100248800	Weak transcription	Gastric	stomach
3	chr15:100213200-100250800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:100213600-100243400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:100219400-100248200	Weak transcription	Small Intestine	intestine
6	chr15:100219600-100248400	Weak transcription	Spleen	Spleen
7	chr15:100219800-100243600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:100222800-100243600	Weak transcription	Brain Angular Gyrus	brain
9	chr15:100223600-100247400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr15:100223800-100243600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:100223800-100246800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr15:100224000-100246600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:100227800-100243600	Weak transcription	HepG2	liver
14	chr15:100231000-100250600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:100231400-100244200	Weak transcription	Stomach Mucosa	stomach
16	chr15:100233200-100243200	Weak transcription	Brain Hippocampus Middle	brain
17	chr15:100233200-100243200	Weak transcription	A549	lung
18	chr15:100233200-100243200	Weak transcription	NHLF	lung
19	chr15:100233200-100246800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr15:100233400-100243400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:100233400-100243600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:100233400-100244200	Weak transcription	Aorta	Aorta
23	chr15:100233400-100244200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr15:100233400-100244400	Weak transcription	Thymus	Thymus
25	chr15:100233400-100247000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:100233400-100247000	Weak transcription	Fetal Stomach	stomach
27	chr15:100233400-100247000	Weak transcription	Left Ventricle	heart
28	chr15:100233400-100247200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:100233400-100247400	Weak transcription	Psoas Muscle	Psoas
30	chr15:100233400-100247600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:100233400-100248400	Weak transcription	Right Ventricle	heart
32	chr15:100233400-100248800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:100233400-100248800	Weak transcription	Esophagus	oesophagus
34	chr15:100233400-100248800	Weak transcription	Fetal Intestine Small	intestine
35	chr15:100233400-100248800	Weak transcription	Lung	lung
36	chr15:100233400-100248800	Weak transcription	Ovary	ovary
37	chr15:100233400-100248800	Weak transcription	Pancreas	Pancrea
38	chr15:100233400-100250600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr15:100233400-100250800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr15:100233400-100251200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr15:100233600-100243000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:100233600-100248800	Weak transcription	Fetal Brain Male	brain
43	chr15:100233800-100243200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:100233800-100243200	Weak transcription	Brain Anterior Caudate	brain
45	chr15:100233800-100243600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr15:100233800-100244000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr15:100233800-100250800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:100233800-100256600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr15:100234000-100243200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr15:100234200-100247000	Weak transcription	Fetal Muscle Leg	muscle

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