Variant report

Variant	rs12565362
Chromosome Location	chr1:70681486-70681487
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:70679382..70681987-chr1:70682758..70684789,3	K562	blood:
2	chr1:70679935..70684301-chr1:70685237..70690690,9	K562	blood:
3	chr1:70680332..70681916-chr1:70685597..70687772,2	MCF-7	breast:
4	chr1:70669364..70673005-chr1:70681293..70684159,5	K562	blood:

Variant related genes	Relation type
ENSG00000228988	Chromatin interaction
ENSG00000066557	Chromatin interaction
ENSG00000116754	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10489927	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10489928	1.00[ASW][hapmap];0.89[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];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12562802	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12566666	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17131235	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17131248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17131251	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2034756	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2210545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2478801	0.83[AMR][1000 genomes]
rs34821575	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35262515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753817	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3767206	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3767207	1.00[ASW][hapmap];0.89[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];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767208	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3920731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41488747	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[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs4649913	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4650031	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55727788	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56902977	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58639674	0.86[ASN][1000 genomes]
rs58696538	0.85[EUR][1000 genomes]
rs58927829	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59234513	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60272091	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60441970	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs632517	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs668525	1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs6702168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716240	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74085992	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74085996	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74085999	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74088004	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74088016	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74088024	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74088029	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs74088032	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74088035	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74088042	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7533067	0.82[CHD][hapmap]

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	esv1798518	chr1:70604106-70723347	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv1797140	chr1:70604106-70724622	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv870841	chr1:70612416-70696554	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv871898	chr1:70681486-70723347	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12565362	SFRS11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70672000-70686200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:70672000-70687000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:70672400-70686800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:70672600-70686400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:70672600-70686600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:70672800-70686600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:70673000-70681800	Weak transcription	Fetal Kidney	kidney
8	chr1:70673000-70683400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:70673200-70686200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:70673200-70686200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:70673200-70686400	Weak transcription	Brain Substantia Nigra	brain
12	chr1:70673200-70686400	Weak transcription	HSMMtube	muscle
13	chr1:70673200-70686600	Weak transcription	NH-A	brain
14	chr1:70673400-70686200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:70673400-70686200	Weak transcription	HMEC	breast
16	chr1:70673400-70686400	Weak transcription	Fetal Brain Male	brain
17	chr1:70673400-70686600	Weak transcription	A549	lung
18	chr1:70673600-70686400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:70673800-70686000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:70673800-70686600	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:70673800-70687200	Weak transcription	Small Intestine	intestine
22	chr1:70674200-70685800	Weak transcription	Right Ventricle	heart
23	chr1:70674200-70686600	Weak transcription	Brain Angular Gyrus	brain
24	chr1:70674200-70686600	Weak transcription	Brain Anterior Caudate	brain
25	chr1:70674200-70686800	Weak transcription	Aorta	Aorta
26	chr1:70674400-70686200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:70674400-70686400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:70674400-70686600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:70674400-70686600	Weak transcription	Colonic Mucosa	Colon
30	chr1:70674400-70686600	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:70674600-70686400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:70674600-70686600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:70675000-70682600	Weak transcription	HSMM	muscle
34	chr1:70675000-70685600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:70675000-70686200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:70675400-70685800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr1:70675400-70686400	Weak transcription	Osteobl	bone
38	chr1:70676000-70686400	Weak transcription	Brain Germinal Matrix	brain
39	chr1:70676200-70681600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:70676200-70686400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:70676400-70686200	Weak transcription	Pancreas	Pancrea
42	chr1:70676400-70686200	Weak transcription	Psoas Muscle	Psoas
43	chr1:70676400-70686200	Weak transcription	Spleen	Spleen
44	chr1:70676400-70686600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr1:70676400-70686600	Weak transcription	NHDF-Ad	bronchial
46	chr1:70676400-70686600	Weak transcription	NHLF	lung
47	chr1:70676400-70686800	Weak transcription	Ovary	ovary
48	chr1:70677400-70681800	Weak transcription	Hela-S3	cervix
49	chr1:70677400-70682800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:70677800-70683200	Strong transcription	Primary T helper cells PMA-I stimulated	--

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