Variant report

Variant	rs10940369
Chromosome Location	chr5:53572117-53572118
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:53566563..53569623-chr5:53569746..53572716,3	K562	blood:
2	chr5:53567065..53579931-chr5:53604839..53612520,32	K562	blood:
3	chr5:53417139..53419799-chr5:53571142..53573081,2	K562	blood:

Variant related genes	Relation type
ENSG00000185305	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10044346	0.84[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[ASN][1000 genomes]
rs10077344	0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10940367	0.92[ASN][1000 genomes]
rs10940368	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10940370	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940371	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10940372	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10940373	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10940374	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11743476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11745511	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12153418	0.99[ASN][1000 genomes]
rs12233919	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12516888	0.94[ASN][1000 genomes]
rs13176320	0.99[ASN][1000 genomes]
rs13180005	0.91[CEU][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13183117	1.00[CHB][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs1445828	0.94[ASN][1000 genomes]
rs166093	0.85[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs17619996	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2289853	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2289854	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2289855	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2289856	0.96[ASN][1000 genomes]
rs2407405	0.84[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs250391	0.90[ASN][1000 genomes]
rs26885	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs26886	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs33282	0.88[ASN][1000 genomes]
rs35918	0.84[ASN][1000 genomes]
rs35921	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs35923	0.94[ASN][1000 genomes]
rs35952	0.93[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs3756481	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs3776641	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3776642	0.97[ASN][1000 genomes]
rs3776644	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3776649	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3797228	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3797230	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3797231	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3797232	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3797233	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3797234	0.94[ASN][1000 genomes]
rs3797235	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3797236	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3797237	0.92[ASN][1000 genomes]
rs3797238	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3857282	0.83[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs388337	0.86[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3910951	0.92[ASN][1000 genomes]
rs4865810	0.92[ASN][1000 genomes]
rs4865812	0.99[ASN][1000 genomes]
rs4865813	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs56854461	0.97[ASN][1000 genomes]
rs6450181	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6450184	0.97[ASN][1000 genomes]
rs67553857	0.96[ASN][1000 genomes]
rs6872062	0.90[ASN][1000 genomes]
rs6872430	0.83[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6883819	0.96[ASN][1000 genomes]
rs6884123	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.99[ASN][1000 genomes]
rs72754232	0.80[ASN][1000 genomes]
rs7704911	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7725454	0.97[ASN][1000 genomes]
rs9292042	0.84[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS 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	29 gene(s)	inside rSNPs	diseases
2	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv881616	chr5:53305742-53639975	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
4	nsv881018	chr5:53305742-53744849	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv880734	chr5:53305742-53770217	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv881161	chr5:53305742-53815495	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
7	nsv881600	chr5:53305742-53823285	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
8	nsv598176	chr5:53311502-53739530	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv880773	chr5:53311918-53815495	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
10	nsv1024303	chr5:53317896-53788276	Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1029224	chr5:53317896-53812899	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
12	nsv949098	chr5:53317990-53816782	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
13	nsv1020517	chr5:53324930-53759046	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
14	nsv1017768	chr5:53326385-53752165	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
15	nsv1032352	chr5:53327170-53762973	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
16	nsv598177	chr5:53333477-53755208	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
17	nsv881056	chr5:53368869-53744849	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
18	nsv881408	chr5:53386267-53815495	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
19	nsv1031072	chr5:53490130-53698866	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
20	nsv880304	chr5:53524508-53727092	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
21	nsv598178	chr5:53566211-53600443	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10940369	C5orf35	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53537400-53575200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr5:53555000-53572400	Weak transcription	Right Ventricle	heart
3	chr5:53555600-53575800	Weak transcription	Primary B cells from cord blood	blood
4	chr5:53558800-53575600	Weak transcription	Aorta	Aorta
5	chr5:53559800-53572200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:53565600-53575200	Weak transcription	Fetal Stomach	stomach
7	chr5:53568200-53595600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:53568400-53573600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:53568600-53573800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:53569000-53575800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr5:53569200-53585600	Weak transcription	Fetal Thymus	thymus
12	chr5:53569600-53579400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:53569800-53572200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:53569800-53574000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:53569800-53583400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr5:53570000-53573600	Weak transcription	Primary T cells from cord blood	blood
17	chr5:53570000-53573800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:53570000-53574000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:53570000-53575600	Weak transcription	Lung	lung
20	chr5:53570000-53581400	Weak transcription	Right Atrium	heart
21	chr5:53570000-53591800	Weak transcription	Gastric	stomach
22	chr5:53570200-53573800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:53570200-53573800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr5:53570200-53573800	Weak transcription	Fetal Intestine Large	intestine
25	chr5:53570200-53573800	Weak transcription	Fetal Intestine Small	intestine
26	chr5:53570200-53573800	Weak transcription	Left Ventricle	heart
27	chr5:53570200-53573800	Weak transcription	Pancreas	Pancrea
28	chr5:53570200-53574000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr5:53570200-53575200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr5:53570600-53581600	Weak transcription	Fetal Lung	lung
31	chr5:53570800-53575200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr5:53571200-53572600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:53571200-53574000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:53571400-53573800	Weak transcription	Placenta	Placenta
35	chr5:53571400-53581600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:53571800-53572200	Enhancers	HMEC	breast
37	chr5:53571800-53573800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr5:53571800-53575800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:53571800-53577200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr5:53572000-53572200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:53572000-53572400	Strong transcription	K562	blood
42	chr5:53572000-53572400	Enhancers	NHEK	skin
43	chr5:53572000-53572600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:53572000-53574400	Weak transcription	H1 Cell Line	embryonic stem cell

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