Variant report

Variant	rs225243
Chromosome Location	chr17:33947212-33947213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:33947002-33949441	K562	blood:	n/a	n/a
2	POLR2A	chr17:33947029-33947618	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:33945134..33947432-chr17:33947574..33949899,2	MCF-7	breast:

Variant related genes	Relation type
AP2B1	TF binding region
ENSG00000006125	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10068	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1037592	0.83[ASN][1000 genomes]
rs11080357	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11653310	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11653357	0.83[ASN][1000 genomes]
rs11655803	0.84[ASN][1000 genomes]
rs11656138	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12604067	0.84[ASN][1000 genomes]
rs12947592	0.83[ASN][1000 genomes]
rs12948669	0.83[ASN][1000 genomes]
rs1671656	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16971217	0.84[ASN][1000 genomes]
rs16971227	0.84[ASN][1000 genomes]
rs17637907	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs225247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225251	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225254	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225259	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225262	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225277	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225295	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225304	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225306	0.98[ASN][1000 genomes]
rs2840044	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28667378	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35237539	0.83[ASN][1000 genomes]
rs7212704	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8069037	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8073935	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9890191	0.82[ASN][1000 genomes]
rs9891574	0.83[ASN][1000 genomes]
rs9891800	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9897552	0.83[ASN][1000 genomes]
rs9899860	0.83[ASN][1000 genomes]
rs9899927	0.83[ASN][1000 genomes]
rs9900378	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9902765	0.81[ASN][1000 genomes]
rs9907772	0.81[ASN][1000 genomes]
rs9908158	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9913003	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9913875	0.83[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	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
5	nsv1062793	chr17:33944732-33976685	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33915600-33954600	Weak transcription	Small Intestine	intestine
2	chr17:33916800-34001200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:33920600-33969800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr17:33920800-33975800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr17:33921000-34024400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:33926000-33955200	Weak transcription	Pancreas	Pancrea
7	chr17:33926800-33952600	Weak transcription	Fetal Brain Male	brain
8	chr17:33931000-34040200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:33933000-33967400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr17:33933000-33997800	Weak transcription	Esophagus	oesophagus
11	chr17:33933600-33952800	Weak transcription	Brain Substantia Nigra	brain
12	chr17:33933600-33967400	Weak transcription	Gastric	stomach
13	chr17:33935000-33951400	Weak transcription	Brain Angular Gyrus	brain
14	chr17:33935600-33953000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr17:33935600-33953400	Weak transcription	HSMMtube	muscle
16	chr17:33936000-33953800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr17:33936800-33956800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr17:33937000-33951000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr17:33937000-33951400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr17:33937000-33951400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr17:33937000-33951800	Weak transcription	HepG2	liver
22	chr17:33937200-33951200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr17:33937200-33951400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr17:33937400-33951400	Weak transcription	Ovary	ovary
25	chr17:33937400-33965000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr17:33938200-33953200	Weak transcription	Colonic Mucosa	Colon
27	chr17:33938400-33951400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr17:33938600-33950600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr17:33938600-33951000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr17:33938600-33951000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr17:33938600-33951200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr17:33938600-33951400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr17:33938600-33951400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr17:33938600-33951400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr17:33938600-33952000	Weak transcription	Fetal Brain Female	brain
36	chr17:33938600-33952800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr17:33938600-33953400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr17:33938600-33953600	Weak transcription	Spleen	Spleen
39	chr17:33938600-33954600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr17:33938800-33951600	Weak transcription	Brain Germinal Matrix	brain
41	chr17:33939000-33953800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr17:33939400-33951400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr17:33939600-33951400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr17:33939800-33951400	Weak transcription	Liver	Liver
45	chr17:33939800-33951400	Weak transcription	Brain Anterior Caudate	brain
46	chr17:33940000-33950200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr17:33940000-33951200	Weak transcription	Adipose Nuclei	Adipose
48	chr17:33940000-33960000	Weak transcription	Right Ventricle	heart
49	chr17:33940200-33947600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr17:33940400-33950600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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