Variant report

Variant	rs2602029
Chromosome Location	chr15:99706633-99706634
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	chr15:99705548..99708454-chr15:99713051..99715766,2	MCF-7	breast:
2	chr15:99697354..99699660-chr15:99705124..99708746,3	K562	blood:

Variant related genes	Relation type
ENSG00000103852	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12915090	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1318292	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1670221	0.81[AMR][1000 genomes]
rs1703767	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1703768	0.86[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2602021	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602034	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes]
rs2623180	0.90[EUR][1000 genomes]
rs2623181	0.91[EUR][1000 genomes]
rs2623184	0.83[CHB][hapmap]
rs2623193	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3803472	0.81[CHD][hapmap]
rs4965445	0.81[GIH][hapmap]
rs7161931	0.80[EUR][1000 genomes]
rs7167303	0.81[CHB][hapmap]
rs8032154	0.80[CHD][hapmap]

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	nsv1050982	chr15:99450004-99725825	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv530685	chr15:99452377-99713365	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2602029	SYNM	cis	cerebellum	SCAN
rs2602029	SYNM	cis	Adipose Subcutaneous	GTEx
rs2602029	TCP1	trans	parietal	SCAN
rs2602029	TTC23	cis	parietal	SCAN
rs2602029	TTC23	cis	Liver	GTEx
rs2602029	TTC23	cis	multi-tissue	Pritchard
rs2602029	RP11-6O2.4	cis	Adipose Subcutaneous	GTEx
rs2602029	SYNM	cis	parietal	SCAN
rs2602029	TTC23	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99665000-99714200	Weak transcription	NHEK	skin
2	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
3	chr15:99678200-99708800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:99684800-99709200	Weak transcription	Colonic Mucosa	Colon
5	chr15:99684800-99721600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:99685000-99720200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:99689600-99707600	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:99689600-99709600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:99689800-99709400	Weak transcription	Brain Angular Gyrus	brain
10	chr15:99690000-99708200	Weak transcription	Right Ventricle	heart
11	chr15:99690000-99709400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr15:99690400-99707400	Weak transcription	Gastric	stomach
13	chr15:99690400-99709800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:99690600-99709000	Weak transcription	Fetal Heart	heart
15	chr15:99692000-99707200	Weak transcription	HSMMtube	muscle
16	chr15:99692000-99717000	Weak transcription	HSMM	muscle
17	chr15:99694800-99711000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr15:99694800-99721200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr15:99694800-99732600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:99694800-99732600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr15:99695200-99721600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr15:99695200-99721800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:99695200-99732400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr15:99696600-99706800	Weak transcription	Osteobl	bone
25	chr15:99696600-99707400	Weak transcription	HepG2	liver
26	chr15:99696600-99709200	Weak transcription	NH-A	brain
27	chr15:99696600-99710800	Weak transcription	HMEC	breast
28	chr15:99697000-99707200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr15:99697000-99716800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:99697000-99756400	Weak transcription	Stomach Mucosa	stomach
31	chr15:99697200-99712400	Weak transcription	Hela-S3	cervix
32	chr15:99698600-99709200	Weak transcription	NHLF	lung
33	chr15:99699000-99708800	Strong transcription	Liver	Liver
34	chr15:99699200-99708400	Weak transcription	Lung	lung
35	chr15:99699400-99731400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:99699600-99707000	Weak transcription	Fetal Thymus	thymus
37	chr15:99699800-99709600	Weak transcription	A549	lung
38	chr15:99700000-99707000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:99700000-99707200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:99700000-99707400	Weak transcription	Brain Substantia Nigra	brain
41	chr15:99700200-99708000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:99700200-99709200	Weak transcription	Aorta	Aorta
43	chr15:99700200-99710800	Weak transcription	Dnd41	blood
44	chr15:99700200-99731200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr15:99700400-99730600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr15:99701400-99707400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:99701800-99709200	Weak transcription	Left Ventricle	heart
48	chr15:99702000-99707200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr15:99702000-99708200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:99702200-99707800	Weak transcription	Brain Anterior Caudate	brain

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