Variant report

Variant	rs6503894
Chromosome Location	chr17:57173845-57173846
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:57172738..57174690-chr17:57176486..57178958,2	K562	blood:
2	chr17:57095356..57201201-chr17:57905452..57953516,1644	MCF-7	breast:
3	chr17:56707711..56710369-chr17:57169547..57176466,6	MCF-7	breast:
4	chr17:57113105..57201250-chr17:57905452..57952793,1492	MCF-7	breast:
5	chr17:57171010..57175734-chr17:57177458..57185228,8	K562	blood:
6	chr17:57173396..57175015-chr17:57227797..57232062,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000108395	Chromatin interaction
ENSG00000224738	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000182628	Chromatin interaction
ENSG00000207996	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11079368	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11654986	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11656413	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11658694	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11658974	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11868348	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12051897	0.80[EUR][1000 genomes]
rs12603238	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12947785	0.81[EUR][1000 genomes]
rs12948746	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1871751	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1967415	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2055779	0.81[EUR][1000 genomes]
rs2158966	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2333410	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3826353	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4500802	0.81[EUR][1000 genomes]
rs4598970	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4932693	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56297715	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56360354	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57869245	0.85[ASN][1000 genomes]
rs58092632	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6416932	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6416933	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6503889	0.80[EUR][1000 genomes]
rs6503890	0.83[EUR][1000 genomes]
rs6503893	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6503896	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7207693	0.81[EUR][1000 genomes]
rs7208505	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7214098	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7214335	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7214892	0.85[EUR][1000 genomes]
rs7218105	0.82[EUR][1000 genomes]
rs72628394	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7503190	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8067264	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8069033	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8072712	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8076121	0.82[EUR][1000 genomes]
rs8081297	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8081967	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8082544	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8182277	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9892795	0.81[EUR][1000 genomes]
rs9898916	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv908643	chr17:56803028-57249010	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
2	nsv908644	chr17:56803028-57371432	Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
3	esv3335958	chr17:56849544-57385398	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	nsv908645	chr17:56857281-57208752	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	150 gene(s)	inside rSNPs	diseases
5	nsv1065063	chr17:56954121-57346694	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
6	nsv1064384	chr17:57049519-57346694	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
7	nsv908646	chr17:57061238-57255810	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases
8	nsv833499	chr17:57070693-57288410	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	208 gene(s)	inside rSNPs	diseases
9	nsv1066388	chr17:57082013-57339981	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	209 gene(s)	inside rSNPs	diseases
10	esv2758462	chr17:57082579-57425634	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	213 gene(s)	inside rSNPs	diseases
11	esv2758699	chr17:57082579-57425634	Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	213 gene(s)	inside rSNPs	diseases
12	nsv1066467	chr17:57117682-57338731	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	200 gene(s)	inside rSNPs	diseases
13	nsv1057209	chr17:57117682-57742240	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
14	nsv543396	chr17:57117682-57742240	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
15	nsv1066788	chr17:57126446-57344129	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS 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 miRNA	193 gene(s)	inside rSNPs	diseases
16	nsv482858	chr17:57136446-57288615	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	184 gene(s)	inside rSNPs	diseases
17	nsv908647	chr17:57165097-57290383	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
18	nsv908648	chr17:57165097-57322954	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	179 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6503894	RAD51C	Cis_1M	lymphoblastoid	RTeQTL
rs6503894	TRIM37	cis	Muscle Skeletal	GTEx
rs6503894	FAM33A	Cis_1M	lymphoblastoid	RTeQTL
rs6503894	TRIM37	cis	Adipose Subcutaneous	GTEx
rs6503894	TRIM37	cis	Whole Blood	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:57121400-57183400	Weak transcription	Gastric	stomach
2	chr17:57121800-57181800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr17:57127000-57181800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr17:57135400-57183400	Weak transcription	Pancreas	Pancrea
5	chr17:57137600-57175800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:57137600-57183000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr17:57151200-57182600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr17:57157800-57176800	Weak transcription	Primary B cells from cord blood	blood
9	chr17:57157800-57181400	Weak transcription	Brain Hippocampus Middle	brain
10	chr17:57165600-57181600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr17:57165800-57181800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr17:57166600-57176800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr17:57167200-57176400	Weak transcription	Right Ventricle	heart
14	chr17:57167400-57175200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr17:57167400-57175600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr17:57167400-57176400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr17:57167400-57177000	Weak transcription	Brain Germinal Matrix	brain
18	chr17:57167400-57177000	Weak transcription	Fetal Intestine Large	intestine
19	chr17:57167400-57177400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr17:57167400-57177400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr17:57167400-57177400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr17:57167400-57177800	Weak transcription	Brain Anterior Caudate	brain
23	chr17:57167400-57181600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr17:57167400-57181800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr17:57167400-57182400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr17:57167400-57183000	Weak transcription	Brain Substantia Nigra	brain
27	chr17:57167400-57183000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr17:57167400-57183400	Weak transcription	Spleen	Spleen
29	chr17:57167600-57176800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr17:57167600-57177000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr17:57167600-57177000	Weak transcription	Fetal Thymus	thymus
32	chr17:57167600-57177200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr17:57167600-57181600	Weak transcription	Fetal Brain Female	brain
34	chr17:57167600-57183000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr17:57167800-57176200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr17:57167800-57177400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr17:57167800-57183000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr17:57168200-57175000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr17:57168200-57177200	Weak transcription	Liver	Liver
40	chr17:57168200-57177400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr17:57168200-57181800	Weak transcription	Thymus	Thymus
42	chr17:57168200-57182600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr17:57168200-57183000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr17:57168400-57175600	Weak transcription	Fetal Intestine Small	intestine
45	chr17:57168400-57176400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr17:57168600-57174600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr17:57168600-57175400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr17:57168600-57176800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr17:57168600-57177000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr17:57168600-57177400	Weak transcription	Monocytes-CD14+_RO01746	blood

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