Variant report

Variant	rs2084900
Chromosome Location	chr15:99774542-99774543
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99773963..99776603-chr15:99777623..99779591,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10152456	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10152794	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12591132	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12593449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1567417	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1567418	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2902154	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55909409	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56315393	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs56341787	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56364603	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62023767	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62025697	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7170360	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7174431	0.90[CHB][hapmap]
rs7175165	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7178124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs735823	0.90[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap]
rs8025136	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8028374	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8029886	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8031175	0.85[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap]
rs8042439	0.96[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8043311	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS 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	60 gene(s)	inside rSNPs	diseases
4	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription 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 miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
9	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
10	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS 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	30 gene(s)	inside rSNPs	diseases
11	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS 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	31 gene(s)	inside rSNPs	diseases
12	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
13	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
14	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
16	nsv1052528	chr15:99736977-99874210	Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
17	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
18	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2084900	SYNM	cis	parietal	SCAN
rs2084900	SYNM	cis	cerebellum	SCAN
rs2084900	LYSMD4	cis	cerebellum	SCAN
rs2084900	TTC23	cis	multi-tissue	Pritchard
rs2084900	TTC23	cis	parietal	SCAN
rs2084900	TTC23	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
2	chr15:99733400-99787400	Weak transcription	NHEK	skin
3	chr15:99749800-99789400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:99750000-99789400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:99756600-99789400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr15:99758600-99789400	Weak transcription	Brain Substantia Nigra	brain
7	chr15:99759200-99788400	Weak transcription	Fetal Thymus	thymus
8	chr15:99759400-99781800	Weak transcription	Spleen	Spleen
9	chr15:99759400-99788600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:99759400-99788600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:99761000-99778400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr15:99761400-99781800	Weak transcription	Pancreas	Pancrea
13	chr15:99761400-99788400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:99762000-99780400	Weak transcription	Esophagus	oesophagus
15	chr15:99762600-99789400	Weak transcription	Gastric	stomach
16	chr15:99762800-99774800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr15:99765400-99784000	Weak transcription	Hela-S3	cervix
18	chr15:99765600-99789400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:99765800-99778600	Weak transcription	Psoas Muscle	Psoas
20	chr15:99765800-99778800	Weak transcription	HUVEC	blood vessel
21	chr15:99765800-99789400	Weak transcription	Lung	lung
22	chr15:99766200-99780000	Weak transcription	Placenta	Placenta
23	chr15:99767000-99778600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr15:99767200-99781400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:99768000-99778200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr15:99768200-99788600	Weak transcription	Colonic Mucosa	Colon
27	chr15:99768200-99789200	Weak transcription	Brain Hippocampus Middle	brain
28	chr15:99768400-99776400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:99768600-99774800	Weak transcription	Fetal Muscle Leg	muscle
30	chr15:99768600-99775000	Weak transcription	Fetal Stomach	stomach
31	chr15:99768600-99776000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr15:99768600-99778600	Weak transcription	Aorta	Aorta
33	chr15:99768600-99780000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:99768600-99780600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:99768600-99780800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr15:99768600-99781000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:99768600-99781000	Weak transcription	Right Ventricle	heart
38	chr15:99768600-99787200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:99768600-99787200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr15:99768600-99787200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:99768600-99787200	Weak transcription	HepG2	liver
42	chr15:99768600-99788400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr15:99768600-99788400	Weak transcription	Ovary	ovary
44	chr15:99768800-99775800	Weak transcription	Fetal Intestine Large	intestine
45	chr15:99768800-99776200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:99768800-99778400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:99768800-99779800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr15:99768800-99780000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr15:99768800-99780600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr15:99768800-99780600	Weak transcription	Fetal Intestine Small	intestine

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