Variant report

Variant	rs1634684
Chromosome Location	chr17:33941051-33941052
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:33932060..33934877-chr17:33939469..33942065,2	MCF-7	breast:
2	chr17:33933800..33936366-chr17:33936981..33942006,8	K562	blood:
3	chr17:33940042..33942067-chr17:33943790..33945473,2	K562	blood:

Variant related genes	Relation type
ENSG00000006125	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1049379	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12150359	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1476553	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs161182	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs161183	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs161184	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs167691	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs178649	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2124246	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2124247	0.83[ASN][1000 genomes]
rs225245	0.89[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs225255	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225269	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs225272	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs225273	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs225281	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs225282	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225284	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225290	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225293	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225297	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225299	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225302	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs226088	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs226426	0.83[ASW][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs226428	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs226432	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs226434	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs226439	0.83[ASW][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs226441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2285742	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2301730	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs321596	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs321599	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs321601	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs321607	0.81[CEU][hapmap];0.81[ASN][1000 genomes]
rs321608	0.81[ASN][1000 genomes]
rs321616	0.85[CEU][hapmap]
rs321617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs321618	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3890901	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4796103	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6505489	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6505490	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6505491	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6505492	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6505493	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71366475	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs720774	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7217565	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7221081	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7221096	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7406966	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8064556	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8067294	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8073375	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8078905	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9635770	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1634684	AP2B1	cis	Muscle Skeletal	GTEx
rs1634684	SLFN5	cis	parietal	SCAN
rs1634684	PEX12	cis	cerebellum	SCAN
rs1634684	TBC1D29	cis	parietal	SCAN
rs1634684	TBC1D29	cis	cerebellum	SCAN

Chromatin state (count:126 , 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	chr17:33916000-33942000	Weak transcription	Right Atrium	heart
3	chr17:33916400-33944800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr17:33916800-33945400	Weak transcription	Stomach Mucosa	stomach
5	chr17:33916800-34001200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr17:33920600-33942200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr17:33920600-33942800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr17:33920600-33944000	Strong transcription	Dnd41	blood
9	chr17:33920600-33969800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr17:33920800-33975800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr17:33921000-33941400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr17:33921000-33942200	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr17:33921000-33943000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr17:33921000-33946200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr17:33921000-33946600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr17:33921000-34024400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr17:33921800-33944000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr17:33924600-33941400	Weak transcription	Psoas Muscle	Psoas
19	chr17:33926000-33955200	Weak transcription	Pancreas	Pancrea
20	chr17:33926200-33943800	Weak transcription	Fetal Heart	heart
21	chr17:33926800-33952600	Weak transcription	Fetal Brain Male	brain
22	chr17:33929800-33942200	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr17:33931000-34040200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr17:33931800-33942400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr17:33932400-33942200	Strong transcription	Fetal Muscle Leg	muscle
26	chr17:33932600-33942000	Strong transcription	Fetal Lung	lung
27	chr17:33932600-33943000	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr17:33933000-33943000	Strong transcription	Osteobl	bone
29	chr17:33933000-33967400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr17:33933000-33997800	Weak transcription	Esophagus	oesophagus
31	chr17:33933600-33941400	Weak transcription	Aorta	Aorta
32	chr17:33933600-33952800	Weak transcription	Brain Substantia Nigra	brain
33	chr17:33933600-33967400	Weak transcription	Gastric	stomach
34	chr17:33934200-33945600	Strong transcription	K562	blood
35	chr17:33934400-33944000	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr17:33935000-33951400	Weak transcription	Brain Angular Gyrus	brain
37	chr17:33935600-33944200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr17:33935600-33953000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr17:33935600-33953400	Weak transcription	HSMMtube	muscle
40	chr17:33936000-33953800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr17:33936200-33941800	Weak transcription	NHLF	lung
42	chr17:33936800-33956800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr17:33937000-33951000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr17:33937000-33951400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr17:33937000-33951400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr17:33937000-33951800	Weak transcription	HepG2	liver
47	chr17:33937200-33947000	Weak transcription	Placenta	Placenta
48	chr17:33937200-33951200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr17:33937200-33951400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr17:33937400-33941400	Weak transcription	Lung	lung

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