Variant report

Variant	rs225306
Chromosome Location	chr17:33920036-33920037
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:33903370..33909494-chr17:33910892..33920548,27	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108733	Chromatin interaction
ENSG00000006125	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10068	0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.86[ASN][1000 genomes]
rs1037590	0.80[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs1037592	0.81[ASN][1000 genomes]
rs10512472	0.80[CHD][hapmap];0.85[JPT][hapmap]
rs11080356	0.90[CEU][hapmap]
rs11080357	0.84[ASN][1000 genomes]
rs11653310	0.82[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap]
rs11653357	0.83[ASN][1000 genomes]
rs11655803	0.82[ASN][1000 genomes]
rs11656138	0.99[ASN][1000 genomes]
rs12452797	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12604067	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12947592	0.81[ASN][1000 genomes]
rs12948669	0.83[ASN][1000 genomes]
rs1671656	0.98[ASN][1000 genomes]
rs16971217	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs16971227	0.82[ASN][1000 genomes]
rs17550632	0.85[CEU][hapmap]
rs17550716	0.90[CEU][hapmap]
rs17637907	0.82[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.83[YRI][hapmap]
rs17638867	0.85[CEU][hapmap]
rs2011897	0.90[CEU][hapmap]
rs225243	0.98[ASN][1000 genomes]
rs225244	0.90[CEU][hapmap]
rs225246	0.90[CEU][hapmap]
rs225247	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[ASN][1000 genomes]
rs225251	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs225254	0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[YRI][hapmap];0.98[ASN][1000 genomes]
rs225259	0.95[ASN][1000 genomes]
rs225262	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225268	0.89[CEU][hapmap]
rs225276	0.90[CEU][hapmap]
rs225277	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225278	0.90[CEU][hapmap]
rs225279	0.90[CEU][hapmap]
rs225295	0.98[ASN][1000 genomes]
rs225304	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs226089	0.90[CEU][hapmap]
rs226090	0.90[CEU][hapmap]
rs2376177	0.87[CEU][hapmap]
rs2840044	0.82[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.83[YRI][hapmap]
rs28667378	0.83[ASN][1000 genomes]
rs35237539	0.83[ASN][1000 genomes]
rs4795086	0.90[CEU][hapmap]
rs4796098	0.90[CEU][hapmap]
rs7211724	0.90[CEU][hapmap]
rs7212704	0.86[ASN][1000 genomes]
rs8069037	0.93[ASN][1000 genomes]
rs8073935	0.90[ASN][1000 genomes]
rs9649	0.90[CEU][hapmap]
rs9890191	0.81[ASN][1000 genomes]
rs9891574	0.81[ASN][1000 genomes]
rs9897552	0.80[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9899860	0.83[ASN][1000 genomes]
rs9899927	0.83[ASN][1000 genomes]
rs9900378	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.99[ASN][1000 genomes]
rs9902765	0.81[ASN][1000 genomes]
rs9913875	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
2	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1060890	chr17:33884124-34011034	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv543318	chr17:33884124-34011034	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs225306	CCL23	cis	parietal	SCAN
rs225306	ZNHIT3	cis	lymphoblastoid	seeQTL
rs225306	AP2B1	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33915000-33922000	Weak transcription	Spleen	Spleen
2	chr17:33915000-33923600	Weak transcription	Gastric	stomach
3	chr17:33915200-33921800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:33915200-33923400	Weak transcription	Colonic Mucosa	Colon
5	chr17:33915200-33923600	Weak transcription	Esophagus	oesophagus
6	chr17:33915200-33923600	Weak transcription	Pancreas	Pancrea
7	chr17:33915200-33930600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:33915200-33932600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr17:33915400-33923600	Weak transcription	Aorta	Aorta
10	chr17:33915600-33920600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr17:33915600-33920800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr17:33915600-33921000	Weak transcription	Placenta	Placenta
13	chr17:33915600-33921200	Weak transcription	Fetal Thymus	thymus
14	chr17:33915600-33921800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr17:33915600-33922200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr17:33915600-33923600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr17:33915600-33954600	Weak transcription	Small Intestine	intestine
18	chr17:33915800-33921000	Weak transcription	HSMMtube	muscle
19	chr17:33915800-33921200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr17:33915800-33921800	Weak transcription	Thymus	Thymus
21	chr17:33915800-33922000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr17:33915800-33922000	Weak transcription	Fetal Muscle Leg	muscle
23	chr17:33915800-33923600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr17:33915800-33923600	Weak transcription	Right Ventricle	heart
25	chr17:33916000-33920600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr17:33916000-33920600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr17:33916000-33921800	Weak transcription	Psoas Muscle	Psoas
28	chr17:33916000-33923800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr17:33916000-33942000	Weak transcription	Right Atrium	heart
30	chr17:33916400-33920800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr17:33916400-33924200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr17:33916400-33944800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr17:33916600-33920600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr17:33916600-33920800	Weak transcription	Primary B cells from cord blood	blood
35	chr17:33916600-33920800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr17:33916600-33921200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr17:33916600-33921200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr17:33916600-33921600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr17:33916600-33921600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr17:33916600-33922000	Weak transcription	Brain Hippocampus Middle	brain
41	chr17:33916600-33923800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr17:33916800-33920600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr17:33916800-33920600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr17:33916800-33920600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr17:33916800-33920800	Weak transcription	Osteobl	bone
46	chr17:33916800-33921000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr17:33916800-33921000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr17:33916800-33921000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr17:33916800-33921000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr17:33916800-33921000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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