Variant report

Variant	rs11577985
Chromosome Location	chr1:211451467-211451468
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:211444424..211446748-chr1:211449200..211451604,3	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11581409	0.88[EUR][1000 genomes]
rs11581989	1.00[ASW][hapmap];0.94[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];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11582143	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs11586974	0.92[YRI][hapmap]
rs11590228	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12041498	0.94[CEU][hapmap];0.85[YRI][hapmap]
rs17017361	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17017394	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17017399	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17017431	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17017432	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.89[LWK][hapmap];0.92[TSI][hapmap]
rs17017441	0.86[LWK][hapmap]
rs17017451	0.85[CHD][hapmap];0.86[LWK][hapmap];0.89[MEX][hapmap]
rs3767380	0.92[YRI][hapmap]
rs55758006	0.83[ASN][1000 genomes]
rs55941941	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56046522	0.83[ASN][1000 genomes]
rs56380051	0.85[ASN][1000 genomes]
rs56381832	0.83[ASN][1000 genomes]
rs57331968	0.85[EUR][1000 genomes]
rs61850980	0.88[ASN][1000 genomes]
rs61850982	0.85[EUR][1000 genomes]
rs61850984	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61850985	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61850986	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61851029	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61851030	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61851033	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6666324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7514863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs7522532	0.83[ASN][1000 genomes]
rs7523875	1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs7538100	0.85[CHD][hapmap];0.86[LWK][hapmap];0.89[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv159013	chr1:211449555-211453750	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11577985	CTSE	cis	parietal	SCAN
rs11577985	LINC00467	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211434400-211453200	Weak transcription	Small Intestine	intestine
2	chr1:211434400-211453400	Weak transcription	Spleen	Spleen
3	chr1:211434400-211454800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:211434400-211487000	Weak transcription	Gastric	stomach
5	chr1:211434600-211453400	Weak transcription	Aorta	Aorta
6	chr1:211434600-211454000	Weak transcription	Pancreas	Pancrea
7	chr1:211434600-211462600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:211434600-211478200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:211434800-211453000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:211434800-211453400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:211434800-211462600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:211434800-211464800	Weak transcription	Right Ventricle	heart
13	chr1:211434800-211474200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:211435600-211460800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:211436200-211456800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:211437000-211454600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:211438800-211478800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:211439800-211478200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:211440000-211458200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:211440600-211454400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:211440800-211481800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:211440800-211483600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr1:211441200-211461200	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:211443000-211480000	Strong transcription	Dnd41	blood
25	chr1:211443000-211480400	Strong transcription	Placenta	Placenta
26	chr1:211443200-211460800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr1:211443200-211484000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:211443600-211454400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:211443800-211460400	Strong transcription	Primary B cells from peripheral blood	blood
30	chr1:211443800-211478200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:211444200-211459400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:211444400-211454000	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:211444400-211479000	Strong transcription	Liver	Liver
34	chr1:211444600-211454400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:211444600-211454400	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:211444600-211457000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:211444600-211457200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:211444600-211459000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:211444600-211459800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:211444600-211471000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:211444600-211478000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:211444600-211479200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr1:211444800-211454600	Strong transcription	K562	blood
44	chr1:211444800-211455400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:211444800-211460600	Strong transcription	HSMM	muscle
46	chr1:211444800-211491200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:211445000-211454000	Strong transcription	NHDF-Ad	bronchial
48	chr1:211445000-211454400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:211445200-211451600	Weak transcription	Brain Germinal Matrix	brain
50	chr1:211445200-211451600	Weak transcription	Left Ventricle	heart

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