Variant report

Variant	rs57098486
Chromosome Location	chr1:70686213-70686214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:70685909-70687757	K562	blood:	n/a	n/a
2	POLR2A	chr1:70684083-70688005	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:70686202-70687877	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:70668667..70673217-chr1:70684547..70688689,8	K562	blood:
2	chr1:70669751..70673129-chr1:70685079..70688457,4	MCF-7	breast:
3	chr1:70684364..70687178-chr1:70692446..70695041,2	MCF-7	breast:
4	chr1:70606579..70609498-chr1:70685222..70687844,2	K562	blood:
5	chr1:70685799..70687948-chr1:70819964..70821804,2	MCF-7	breast:
6	chr1:70667153..70674800-chr1:70681943..70693478,26	K562	blood:
7	chr1:70685268..70690578-chr1:70702989..70707451,6	MCF-7	breast:
8	chr1:70670643..70672906-chr1:70684026..70686642,2	MCF-7	breast:

No data

Variant related genes	Relation type
SRSF11	TF binding region
ENSG00000118454	Chromatin interaction
ENSG00000197568	Chromatin interaction
ENSG00000033122	Chromatin interaction
ENSG00000116754	Chromatin interaction
ENSG00000066557	Chromatin interaction

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

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

rs_ID	r²[population]
rs1412867	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17131236	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17131238	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17131241	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34121744	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35522955	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3753818	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs476591	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs522320	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs549843	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56299138	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56873377	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs587567	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60409157	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60598073	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs610953	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61785267	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61785269	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61785270	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61785272	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs632047	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs651717	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs666163	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6664084	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6664480	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6666941	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6700543	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs676753	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74085998	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7533067	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[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	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
rs57098486	SFRS11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70672000-70687000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:70672400-70686800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:70672600-70686400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr1:70672600-70686600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:70672800-70686600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:70673200-70686400	Weak transcription	Brain Substantia Nigra	brain
7	chr1:70673200-70686400	Weak transcription	HSMMtube	muscle
8	chr1:70673200-70686600	Weak transcription	NH-A	brain
9	chr1:70673400-70686400	Weak transcription	Fetal Brain Male	brain
10	chr1:70673400-70686600	Weak transcription	A549	lung
11	chr1:70673600-70686400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:70673800-70686600	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:70673800-70687200	Weak transcription	Small Intestine	intestine
14	chr1:70674200-70686600	Weak transcription	Brain Angular Gyrus	brain
15	chr1:70674200-70686600	Weak transcription	Brain Anterior Caudate	brain
16	chr1:70674200-70686800	Weak transcription	Aorta	Aorta
17	chr1:70674400-70686400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:70674400-70686600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:70674400-70686600	Weak transcription	Colonic Mucosa	Colon
20	chr1:70674400-70686600	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:70674600-70686400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:70674600-70686600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:70675400-70686400	Weak transcription	Osteobl	bone
24	chr1:70676000-70686400	Weak transcription	Brain Germinal Matrix	brain
25	chr1:70676200-70686400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:70676400-70686600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:70676400-70686600	Weak transcription	NHDF-Ad	bronchial
28	chr1:70676400-70686600	Weak transcription	NHLF	lung
29	chr1:70676400-70686800	Weak transcription	Ovary	ovary
30	chr1:70679600-70686600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:70681600-70686400	Weak transcription	Fetal Brain Female	brain
32	chr1:70681800-70687200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:70682000-70686400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:70682000-70686400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:70682000-70686400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:70682000-70686600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:70682000-70686600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:70682200-70686400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:70682200-70686400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:70682200-70686600	Weak transcription	GM12878-XiMat	blood
41	chr1:70682400-70686400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:70682400-70686400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:70682400-70686400	Weak transcription	Fetal Lung	lung
44	chr1:70682400-70686800	Weak transcription	Esophagus	oesophagus
45	chr1:70682400-70687000	Weak transcription	Gastric	stomach
46	chr1:70682400-70687200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr1:70682600-70686400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:70682600-70686400	Weak transcription	Adipose Nuclei	Adipose
49	chr1:70682600-70686400	Weak transcription	Fetal Intestine Large	intestine
50	chr1:70682600-70686400	Weak transcription	Placenta	Placenta

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