Variant report

Variant	rs9516870
Chromosome Location	chr13:97864433-97864434
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:97854002..97856738-chr13:97861937..97864519,2	K562	blood:
2	chr13:97863456..97868216-chr13:97870122..97874469,4	MCF-7	breast:
3	chr13:97863320..97866050-chr13:97870131..97873643,3	K562	blood:
4	chr13:97857393..97860192-chr13:97862596..97865751,4	K562	blood:
5	chr13:97862725..97864996-chr13:97866884..97868845,2	K562	blood:

Variant related genes	Relation type
ENSG00000139793	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10220223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410758	0.90[ASN][1000 genomes]
rs17235537	0.90[ASN][1000 genomes]
rs17235551	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17301278	0.86[ASN][1000 genomes]
rs17301299	0.90[ASN][1000 genomes]
rs17301306	0.90[ASN][1000 genomes]
rs3825522	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4120984	0.90[ASN][1000 genomes]
rs5024203	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57348783	0.86[ASN][1000 genomes]
rs57806253	0.86[ASN][1000 genomes]
rs61107763	0.86[ASN][1000 genomes]
rs6491338	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6491339	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6491341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7317904	0.86[ASN][1000 genomes]
rs7329695	0.86[MKK][hapmap];0.84[TSI][hapmap]
rs7338056	0.85[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.86[ASN][1000 genomes]
rs7983632	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7984898	0.91[ASN][1000 genomes]
rs7988998	0.86[ASN][1000 genomes]
rs7989356	0.86[ASN][1000 genomes]
rs7990235	0.86[ASN][1000 genomes]
rs7990802	0.86[ASN][1000 genomes]
rs7991020	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7997476	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8000282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9513214	0.86[ASN][1000 genomes]
rs9513215	0.86[ASN][1000 genomes]
rs9513216	0.86[ASN][1000 genomes]
rs9513219	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9513221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9516845	0.86[ASN][1000 genomes]
rs9516846	0.84[ASN][1000 genomes]
rs9516847	0.86[ASN][1000 genomes]
rs9516848	0.85[ASN][1000 genomes]
rs9516849	0.86[ASN][1000 genomes]
rs9516850	0.86[ASN][1000 genomes]
rs9516853	0.86[ASN][1000 genomes]
rs9516857	0.81[MKK][hapmap]
rs9516864	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516867	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9516872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9516873	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9584530	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9516870	RAP2A	cis	parietal	SCAN
rs9516870	GPC5	cis	parietal	SCAN
rs9516870	TGDS	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:97858600-97867200	Weak transcription	Hela-S3	cervix
2	chr13:97861400-97865000	Enhancers	Dnd41	blood
3	chr13:97861600-97865200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr13:97861600-97865400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:97862000-97865000	Enhancers	Fetal Thymus	thymus
6	chr13:97862000-97865400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr13:97862000-97865600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr13:97862400-97865400	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr13:97862800-97865200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr13:97862800-97865200	Enhancers	HMEC	breast
11	chr13:97863000-97864600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr13:97863000-97864800	Enhancers	Placenta Amnion	Placenta Amnion
13	chr13:97863000-97865000	Enhancers	Brain Cingulate Gyrus	brain
14	chr13:97863000-97865000	Enhancers	Ovary	ovary
15	chr13:97863000-97865400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr13:97863000-97865400	Enhancers	Brain Hippocampus Middle	brain
17	chr13:97863200-97865000	Weak transcription	GM12878-XiMat	blood
18	chr13:97863200-97865200	Enhancers	Brain Substantia Nigra	brain
19	chr13:97863400-97864600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr13:97863400-97865200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr13:97863600-97864600	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr13:97863600-97864800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr13:97863600-97865000	Enhancers	Adipose Nuclei	Adipose
24	chr13:97863600-97865400	Enhancers	Brain Anterior Caudate	brain
25	chr13:97863600-97866600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr13:97863600-97866800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr13:97863600-97866800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr13:97863600-97867000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr13:97863800-97864600	Weak transcription	NH-A	brain
30	chr13:97863800-97866600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr13:97863800-97866600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr13:97863800-97866800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr13:97863800-97866800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr13:97863800-97866800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr13:97863800-97866800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr13:97863800-97866800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr13:97863800-97866800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr13:97863800-97867000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr13:97864000-97864600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
40	chr13:97864000-97865200	Enhancers	Primary T cells from cord blood	blood
41	chr13:97864000-97865200	Enhancers	HepG2	liver
42	chr13:97864000-97866800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr13:97864200-97864600	Enhancers	Duodenum Mucosa	Duodenum
44	chr13:97864200-97864800	Enhancers	Fetal Intestine Small	intestine
45	chr13:97864200-97865000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr13:97864200-97865000	Enhancers	Placenta	Placenta
47	chr13:97864200-97865400	Enhancers	K562	blood
48	chr13:97864400-97864600	Enhancers	HSMMtube	muscle
49	chr13:97864400-97865000	Enhancers	Left Ventricle	heart
50	chr13:97864400-97865200	Enhancers	Stomach Mucosa	stomach

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