Variant report

Variant	rs60409157
Chromosome Location	chr1:70636364-70636365
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:70610824..70612517-chr1:70634874..70637196,2	K562	blood:
2	chr1:70635318..70637973-chr1:70641469..70643129,2	K562	blood:
3	chr1:70634010..70636931-chr1:70644146..70645771,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1412867	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17131236	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17131238	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17131241	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34121744	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35522955	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753818	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs476591	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs522320	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs549843	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56299138	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56873377	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57098486	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs587567	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60598073	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs610953	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61785267	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61785269	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61785270	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61785272	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs632047	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs651717	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs666163	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6664084	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6664480	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6666941	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6700543	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs676753	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74085998	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533067	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[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	nsv531879	chr1:70386455-70644617	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60409157	SFRS11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70601000-70643200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr1:70601200-70652000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:70603400-70648800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:70605400-70639400	Weak transcription	Brain Anterior Caudate	brain
5	chr1:70606800-70651600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:70606800-70661800	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:70607000-70670200	Weak transcription	Psoas Muscle	Psoas
8	chr1:70607000-70670400	Weak transcription	Small Intestine	intestine
9	chr1:70607200-70652600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:70607400-70655200	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:70608200-70645400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:70608400-70653400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:70608800-70654800	Weak transcription	Thymus	Thymus
14	chr1:70608800-70655800	Weak transcription	Esophagus	oesophagus
15	chr1:70609200-70647600	Weak transcription	Colonic Mucosa	Colon
16	chr1:70609200-70650200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:70609400-70638800	Weak transcription	Placenta	Placenta
18	chr1:70609400-70649800	Weak transcription	Fetal Brain Male	brain
19	chr1:70609600-70661200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:70610000-70642600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:70610000-70656600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:70610000-70667800	Weak transcription	HepG2	liver
23	chr1:70610400-70650200	Weak transcription	GM12878-XiMat	blood
24	chr1:70610400-70653600	Weak transcription	Gastric	stomach
25	chr1:70610600-70669600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:70611000-70666600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:70611200-70645000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:70611200-70670400	Weak transcription	Pancreas	Pancrea
29	chr1:70611400-70652800	Weak transcription	Spleen	Spleen
30	chr1:70611600-70643000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:70612400-70669000	Weak transcription	HUVEC	blood vessel
32	chr1:70613000-70649200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:70613400-70638000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:70613400-70658400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr1:70613600-70657000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:70613600-70667800	Weak transcription	Brain Angular Gyrus	brain
37	chr1:70613800-70643000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr1:70613800-70645200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr1:70613800-70649200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:70613800-70658000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:70614400-70651000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:70614400-70657800	Weak transcription	Fetal Kidney	kidney
43	chr1:70615000-70670000	Weak transcription	NH-A	brain
44	chr1:70615000-70670400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:70615200-70637200	Weak transcription	HSMM	muscle
46	chr1:70615200-70643000	Weak transcription	Ovary	ovary
47	chr1:70615200-70649200	Weak transcription	Left Ventricle	heart
48	chr1:70616400-70649200	Weak transcription	Fetal Lung	lung
49	chr1:70616600-70637200	Weak transcription	Adipose Nuclei	Adipose
50	chr1:70616600-70637800	Weak transcription	Dnd41	blood

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