Variant report

Variant	rs10930857
Chromosome Location	chr2:180090978-180090979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10084229	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10170430	0.97[ASN][1000 genomes]
rs10196577	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10197425	0.94[ASN][1000 genomes]
rs10205477	0.85[ASN][1000 genomes]
rs10208593	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10439300	0.86[JPT][hapmap]
rs10803924	0.85[JPT][hapmap]
rs10930855	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10930856	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs12621023	0.86[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12693175	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12693178	0.81[YRI][hapmap]
rs12693180	0.91[ASN][1000 genomes]
rs12989055	0.91[ASN][1000 genomes]
rs12997079	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13022867	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs13029576	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13389956	0.91[ASN][1000 genomes]
rs13396334	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13403231	0.88[ASN][1000 genomes]
rs13404037	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13420582	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13427714	0.84[ASN][1000 genomes]
rs17363260	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17363267	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs17454311	0.86[JPT][hapmap];0.88[YRI][hapmap]
rs1968618	0.84[YRI][hapmap]
rs2289993	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs2289994	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs28763731	0.88[ASN][1000 genomes]
rs340320	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs340332	0.86[JPT][hapmap]
rs340334	0.86[JPT][hapmap]
rs35539795	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4894081	0.81[YRI][hapmap]
rs56181927	0.88[ASN][1000 genomes]
rs67028844	0.88[ASN][1000 genomes]
rs9288025	0.86[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv3061	chr2:180057194-180095718	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3341806	chr2:180070495-180093344	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv1798738	chr2:180084168-180100584	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10930857	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180067600-180097600	Weak transcription	Primary B cells from cord blood	blood
2	chr2:180067600-180104600	Weak transcription	Fetal Kidney	kidney
3	chr2:180068000-180103800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:180068400-180092800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:180083800-180091000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:180083800-180092000	Weak transcription	Aorta	Aorta
7	chr2:180083800-180102200	Weak transcription	HMEC	breast
8	chr2:180084000-180091000	Weak transcription	Small Intestine	intestine
9	chr2:180084200-180091000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:180085200-180091200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:180085400-180091200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:180087200-180097600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr2:180087400-180094800	Weak transcription	Osteobl	bone
14	chr2:180087600-180091000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:180087600-180095800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:180088400-180093000	Enhancers	Brain Cingulate Gyrus	brain
17	chr2:180088600-180092200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:180088800-180091200	Enhancers	Colon Smooth Muscle	Colon
19	chr2:180088800-180098400	Weak transcription	Spleen	Spleen
20	chr2:180089000-180091000	Enhancers	Brain Substantia Nigra	brain
21	chr2:180089000-180091800	Enhancers	Brain Angular Gyrus	brain
22	chr2:180089000-180093000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:180089000-180093000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr2:180089000-180093000	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr2:180089000-180093400	Enhancers	Brain Anterior Caudate	brain
26	chr2:180089200-180091200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:180089200-180092400	Weak transcription	Ovary	ovary
28	chr2:180089400-180091200	Enhancers	Right Ventricle	heart
29	chr2:180089600-180091000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:180089600-180091200	Weak transcription	Fetal Heart	heart
31	chr2:180089600-180091200	Enhancers	Left Ventricle	heart
32	chr2:180089600-180092000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr2:180089600-180095000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:180089600-180115200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:180089800-180091600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr2:180089800-180091600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:180089800-180095000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr2:180089800-180095000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr2:180089800-180100200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:180089800-180100200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr2:180089800-180102000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:180090000-180091600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:180090000-180092600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:180090000-180093800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr2:180090000-180098400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:180090000-180102000	Weak transcription	Fetal Muscle Leg	muscle
47	chr2:180090200-180091000	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr2:180090200-180092200	Enhancers	Brain Germinal Matrix	brain
49	chr2:180090400-180091000	Enhancers	Stomach Smooth Muscle	stomach
50	chr2:180090400-180091600	Enhancers	Right Atrium	heart

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