Variant report

Variant	rs34627893
Chromosome Location	chr17:37570737-37570738
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:37557980..37559708-chr17:37570144..37572871,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266469	Chromatin interaction
ENSG00000108306	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10221223	0.82[EUR][1000 genomes]
rs10445305	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10445306	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10491128	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10491129	0.81[EUR][1000 genomes]
rs11078898	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11078900	0.80[EUR][1000 genomes]
rs11650081	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11650146	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11651089	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11659010	0.82[ASN][1000 genomes]
rs11867312	0.84[EUR][1000 genomes]
rs11868133	0.87[ASN][1000 genomes]
rs11869109	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11869259	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11869323	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12150493	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12452509	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12452880	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12600625	0.84[ASN][1000 genomes]
rs12600751	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12937703	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12938268	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12939831	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12943928	0.81[EUR][1000 genomes]
rs12947620	0.82[EUR][1000 genomes]
rs12948560	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12950666	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13341996	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2024073	0.81[EUR][1000 genomes]
rs2338797	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2338798	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2338800	0.84[EUR][1000 genomes]
rs34363096	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34432983	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34597616	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35285898	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35546703	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35667594	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36064019	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4390625	0.81[EUR][1000 genomes]
rs4410117	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4511574	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4794807	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4794809	0.81[ASN][1000 genomes]
rs4794810	0.84[EUR][1000 genomes]
rs4795356	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4795357	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4795359	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4795361	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4795362	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4795364	0.84[ASN][1000 genomes]
rs55722796	0.80[EUR][1000 genomes]
rs57399933	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs583980	0.81[EUR][1000 genomes]
rs585961	0.81[EUR][1000 genomes]
rs612209	0.80[EUR][1000 genomes]
rs620686	0.81[EUR][1000 genomes]
rs638201	0.81[EUR][1000 genomes]
rs650106	0.81[EUR][1000 genomes]
rs6503502	0.84[EUR][1000 genomes]
rs6503503	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6503506	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6503507	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6503513	0.87[ASN][1000 genomes]
rs6503515	0.81[EUR][1000 genomes]
rs68178216	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7208274	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7208714	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7210488	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7218074	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7218484	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7218670	0.84[EUR][1000 genomes]
rs7220650	0.83[EUR][1000 genomes]
rs7221875	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7223331	0.83[EUR][1000 genomes]
rs7223438	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73293051	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7359658	0.84[EUR][1000 genomes]
rs7405667	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7501488	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs801420	0.80[EUR][1000 genomes]
rs8065879	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8069451	0.83[EUR][1000 genomes]
rs8070695	0.82[EUR][1000 genomes]
rs8072351	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8076494	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8076546	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8077104	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8079303	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8079560	0.84[EUR][1000 genomes]
rs8081033	0.84[EUR][1000 genomes]
rs8081220	0.81[EUR][1000 genomes]
rs9892055	0.84[EUR][1000 genomes]
rs9892675	0.86[ASN][1000 genomes]
rs9894500	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9894586	0.84[EUR][1000 genomes]
rs9894864	0.84[EUR][1000 genomes]
rs9896913	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9898170	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9898773	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9901219	0.87[ASN][1000 genomes]
rs9903363	0.84[EUR][1000 genomes]
rs9904334	0.81[EUR][1000 genomes]
rs9904919	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9905432	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9905617	0.84[EUR][1000 genomes]
rs9908760	0.84[EUR][1000 genomes]
rs9909064	0.84[EUR][1000 genomes]
rs9944411	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932024	chr17:37192290-37850932	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
2	nsv1060126	chr17:37333956-37659189	Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
3	nsv1057655	chr17:37333956-37732451	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
4	nsv1066033	chr17:37333956-37795617	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
5	nsv543340	chr17:37333956-37795617	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
6	nsv908204	chr17:37349655-37682657	Genic enhancers Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
7	nsv1057057	chr17:37395082-37627025	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1061951	chr17:37442228-37770903	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
9	nsv543341	chr17:37442228-37770903	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
10	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
11	nsv532712	chr17:37521822-37768345	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34627893	CRKRS	Cis_1M	lymphoblastoid	RTeQTL
rs34627893	PGAP3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37558400-37583800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:37559000-37571000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr17:37559000-37571200	Weak transcription	Right Atrium	heart
4	chr17:37559000-37606600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr17:37559200-37571200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr17:37560800-37605000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:37560800-37605400	Strong transcription	Fetal Thymus	thymus
8	chr17:37560800-37605600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr17:37561000-37578400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr17:37561000-37585200	Strong transcription	Brain Germinal Matrix	brain
11	chr17:37561000-37604800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr17:37561000-37604800	Strong transcription	Placenta	Placenta
13	chr17:37561000-37605200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr17:37561000-37605400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr17:37561200-37576600	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr17:37561200-37578400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr17:37561200-37578400	Strong transcription	Fetal Muscle Leg	muscle
18	chr17:37561200-37604400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr17:37561200-37604600	Strong transcription	Liver	Liver
20	chr17:37561200-37605000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr17:37561200-37605200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr17:37561400-37588200	Strong transcription	HepG2	liver
23	chr17:37561400-37595400	Strong transcription	Thymus	Thymus
24	chr17:37561400-37604800	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr17:37561400-37604800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr17:37561400-37605000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr17:37561600-37604600	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr17:37561600-37605600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr17:37561800-37577000	Strong transcription	Dnd41	blood
30	chr17:37561800-37587600	Strong transcription	Primary T cells from cord blood	blood
31	chr17:37561800-37604400	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr17:37562000-37604400	Strong transcription	Adipose Nuclei	Adipose
33	chr17:37562000-37604600	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr17:37562000-37604600	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr17:37562200-37576200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr17:37562200-37604200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr17:37562200-37604400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr17:37562200-37604600	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr17:37562400-37576400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr17:37562400-37604200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr17:37562400-37604600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr17:37562400-37604600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr17:37562600-37584000	Strong transcription	Osteobl	bone
44	chr17:37562600-37604200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr17:37562800-37572000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr17:37562800-37600400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr17:37563000-37586200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr17:37563000-37604600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr17:37563000-37604800	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr17:37563600-37578000	Strong transcription	Fetal Intestine Large	intestine

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