Variant report

Variant	rs10857964
Chromosome Location	chr1:113097633-113097634
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10857961	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10857967	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11102496	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11102498	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11102501	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11102509	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11102513	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11102514	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12029985	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12040988	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12045227	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12049572	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12117479	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12122980	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12130243	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12137269	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12140506	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12406530	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12724928	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12728311	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2064711	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2273368	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2887882	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34107138	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34569066	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35023236	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35147679	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3737136	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55652172	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56135413	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60900293	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9308256	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10857964	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs10857964	ST7L	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113058800-113119400	Weak transcription	HepG2	liver
2	chr1:113060200-113132400	Weak transcription	Pancreas	Pancrea
3	chr1:113062400-113117400	Weak transcription	Psoas Muscle	Psoas
4	chr1:113064400-113132200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:113065200-113114800	Weak transcription	Small Intestine	intestine
6	chr1:113065400-113114600	Weak transcription	Fetal Brain Male	brain
7	chr1:113066000-113114600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:113066000-113132200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:113066200-113114400	Weak transcription	Dnd41	blood
10	chr1:113067000-113117400	Weak transcription	Fetal Thymus	thymus
11	chr1:113068000-113100200	Weak transcription	Fetal Heart	heart
12	chr1:113070400-113120600	Weak transcription	Right Ventricle	heart
13	chr1:113070600-113111600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:113070600-113112400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:113070600-113112400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:113070600-113117800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:113070600-113120200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:113070600-113132400	Weak transcription	Aorta	Aorta
19	chr1:113072000-113114400	Weak transcription	Brain Anterior Caudate	brain
20	chr1:113076400-113115200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:113080200-113117800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:113080800-113117400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:113081200-113132200	Weak transcription	Primary B cells from cord blood	blood
24	chr1:113081400-113132400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:113081800-113132200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:113082000-113106600	Weak transcription	Fetal Kidney	kidney
27	chr1:113082000-113116000	Weak transcription	Left Ventricle	heart
28	chr1:113082000-113117400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:113082200-113118000	Weak transcription	Lung	lung
30	chr1:113083200-113123200	Weak transcription	Right Atrium	heart
31	chr1:113083600-113111600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:113083600-113114400	Weak transcription	Fetal Brain Female	brain
33	chr1:113083600-113117400	Weak transcription	Brain Angular Gyrus	brain
34	chr1:113084000-113114600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:113084000-113131400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:113084200-113104400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:113084200-113110200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:113084200-113114800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr1:113084200-113117400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:113084200-113117400	Weak transcription	Brain Germinal Matrix	brain
41	chr1:113084200-113118000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr1:113084600-113106400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:113084600-113113800	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:113084600-113114400	Weak transcription	Primary T cells from cord blood	blood
45	chr1:113084600-113114600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:113084600-113120600	Weak transcription	Ovary	ovary
47	chr1:113084800-113137000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr1:113085000-113109800	Weak transcription	Fetal Lung	lung
49	chr1:113085200-113103200	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:113085200-113114600	Weak transcription	Placenta	Placenta

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