Variant report

Variant	rs12949537
Chromosome Location	chr17:16240488-16240489
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	chr17:16117546..16120375-chr17:16238213..16240874,2	MCF-7	breast:
2	chr17:16230260..16232698-chr17:16238773..16240667,2	K562	blood:

Variant related genes	Relation type
ENSG00000141027	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11650283	0.80[EUR][1000 genomes]
rs11651955	0.81[EUR][1000 genomes]
rs11655906	0.93[EUR][1000 genomes]
rs11655907	0.93[EUR][1000 genomes]
rs12449629	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12945877	0.80[EUR][1000 genomes]
rs12946717	0.81[EUR][1000 genomes]
rs12947973	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12948680	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12949255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12949375	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2074995	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28516015	0.82[EUR][1000 genomes]
rs28862997	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095171	0.81[EUR][1000 genomes]
rs3112511	0.82[EUR][1000 genomes]
rs3112513	0.82[EUR][1000 genomes]
rs35762856	0.80[EUR][1000 genomes]
rs4792735	0.93[EUR][1000 genomes]
rs7224367	0.86[EUR][1000 genomes]
rs9890539	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9893005	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers 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	120 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12949537	ZSWIM7	cis	Muscle Skeletal	GTEx
rs12949537	ADORA2B	cis	Muscle Skeletal	GTEx
rs12949537	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs12949537	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs12949537	ADORA2B	cis	Nerve Tibial	GTEx
rs12949537	ADORA2B	cis	Artery Tibial	GTEx
rs12949537	ADORA2B	cis	Esophagus Muscularis	GTEx
rs12949537	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs12949537	ADORA2B	cis	Thyroid	GTEx
rs12949537	CENPV	cis	Artery Tibial	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16201600-16246400	Weak transcription	Fetal Brain Male	brain
2	chr17:16205800-16245600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr17:16206000-16245800	Weak transcription	Brain Anterior Caudate	brain
4	chr17:16206000-16246000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr17:16209000-16245600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr17:16214600-16255200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:16217000-16246000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr17:16217200-16255200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr17:16219200-16246000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr17:16222800-16245600	Weak transcription	Right Ventricle	heart
11	chr17:16225800-16245800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr17:16226600-16245600	Weak transcription	Fetal Kidney	kidney
13	chr17:16229400-16255600	Weak transcription	Esophagus	oesophagus
14	chr17:16230200-16246000	Weak transcription	Spleen	Spleen
15	chr17:16230400-16245600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr17:16230400-16245600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr17:16230400-16245600	Weak transcription	Brain Germinal Matrix	brain
18	chr17:16230400-16245600	Weak transcription	Placenta	Placenta
19	chr17:16230400-16246000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr17:16230400-16246200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr17:16230400-16253600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr17:16230400-16255000	Weak transcription	Primary B cells from cord blood	blood
23	chr17:16230400-16255200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr17:16230400-16255200	Weak transcription	Brain Substantia Nigra	brain
25	chr17:16230600-16243800	Weak transcription	Thymus	Thymus
26	chr17:16230600-16244000	Weak transcription	Primary T cells from cord blood	blood
27	chr17:16230600-16245400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr17:16230600-16245600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:16230600-16245600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr17:16230600-16245600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr17:16230600-16245600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr17:16230600-16245600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr17:16230600-16245600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr17:16230600-16245600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr17:16230600-16245600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr17:16230600-16245600	Weak transcription	Fetal Thymus	thymus
37	chr17:16230600-16245600	Weak transcription	Left Ventricle	heart
38	chr17:16230600-16245800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr17:16230600-16245800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr17:16230600-16245800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr17:16230600-16245800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr17:16230600-16245800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr17:16230600-16246000	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr17:16230600-16246000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr17:16230600-16246000	Weak transcription	Brain Hippocampus Middle	brain
46	chr17:16230600-16246000	Weak transcription	Dnd41	blood
47	chr17:16230600-16246400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr17:16230600-16250800	Weak transcription	Brain Angular Gyrus	brain
49	chr17:16230600-16254200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr17:16230600-16255200	Weak transcription	Colon Smooth Muscle	Colon

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