Variant report

Variant	rs1002171
Chromosome Location	chr11:71217571-71217572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11233868	0.84[EUR][1000 genomes]
rs11233947	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11501814	0.92[EUR][1000 genomes]
rs12273154	0.84[EUR][1000 genomes]
rs12275121	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12275635	0.84[EUR][1000 genomes]
rs12275636	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12277408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12283114	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12283177	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12283185	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12286569	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12286616	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs12288906	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12289036	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12289074	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12574206	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs12574554	0.84[EUR][1000 genomes]
rs12575605	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12575622	0.88[EUR][1000 genomes]
rs12576621	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs12577807	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17161576	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17161578	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1893058	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2298776	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs28722015	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28823295	0.84[EUR][1000 genomes]
rs28898287	0.84[EUR][1000 genomes]
rs3794062	0.84[EUR][1000 genomes]
rs3794064	0.84[EUR][1000 genomes]
rs3814733	0.84[EUR][1000 genomes]
rs4316537	1.00[CEU][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap]
rs57017893	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57197278	0.84[EUR][1000 genomes]
rs57500217	0.84[EUR][1000 genomes]
rs57557229	0.84[EUR][1000 genomes]
rs57718633	0.94[EUR][1000 genomes]
rs58615796	0.88[EUR][1000 genomes]
rs59379414	0.84[EUR][1000 genomes]
rs59422671	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59487812	0.84[EUR][1000 genomes]
rs59511885	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59972361	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114525	0.84[EUR][1000 genomes]
rs7120978	0.84[EUR][1000 genomes]
rs7121106	0.84[EUR][1000 genomes]
rs7122671	1.00[CEU][hapmap]
rs7129044	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs7130479	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7483469	0.86[EUR][1000 genomes]
rs753352	0.82[EUR][1000 genomes]
rs7940351	0.94[EUR][1000 genomes]
rs7943296	0.83[EUR][1000 genomes]
rs7952035	1.00[CEU][hapmap];0.84[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	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv897897	chr11:71088949-71217571	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
4	nsv468632	chr11:71200320-71289089	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv555402	chr11:71200320-71289089	Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1002171	NADSYN1	cis	Artery Tibial	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71165800-71218400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr11:71181400-71217800	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr11:71181800-71218000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr11:71182000-71217600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr11:71182200-71217800	Strong transcription	Primary T cells from cord blood	blood
6	chr11:71182400-71217600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr11:71182400-71217800	Strong transcription	Duodenum Mucosa	Duodenum
8	chr11:71189800-71218400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr11:71199600-71218400	Strong transcription	Fetal Intestine Small	intestine
10	chr11:71209400-71218800	Weak transcription	Small Intestine	intestine
11	chr11:71210200-71217600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:71210400-71217800	Weak transcription	Osteobl	bone
13	chr11:71210400-71220200	Weak transcription	NHEK	skin
14	chr11:71210600-71219200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr11:71211600-71218800	Weak transcription	HMEC	breast
16	chr11:71211800-71220600	Weak transcription	NH-A	brain
17	chr11:71211800-71232400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr11:71212000-71218200	Weak transcription	HSMMtube	muscle
19	chr11:71212000-71220600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr11:71212200-71218200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr11:71213000-71219600	Weak transcription	Primary B cells from cord blood	blood
22	chr11:71213000-71220800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr11:71213200-71217600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr11:71213200-71218200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:71213200-71220600	Weak transcription	Colon Smooth Muscle	Colon
26	chr11:71213200-71232200	Weak transcription	Brain Angular Gyrus	brain
27	chr11:71213400-71219200	Weak transcription	HepG2	liver
28	chr11:71213600-71218400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:71213800-71217800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr11:71214000-71217800	Strong transcription	Liver	Liver
31	chr11:71214000-71218400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr11:71214600-71218000	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr11:71214600-71220000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr11:71214800-71219400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr11:71215000-71217800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr11:71215000-71222400	Weak transcription	HSMM	muscle
37	chr11:71215200-71217600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr11:71215400-71217800	Weak transcription	Placenta	Placenta
39	chr11:71215400-71218800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:71215400-71219600	Weak transcription	Left Ventricle	heart
41	chr11:71215600-71218000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr11:71215600-71219400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr11:71215600-71220600	Weak transcription	Colonic Mucosa	Colon
44	chr11:71215600-71236600	Weak transcription	Brain Anterior Caudate	brain
45	chr11:71215800-71218400	Weak transcription	Fetal Thymus	thymus
46	chr11:71215800-71218400	Weak transcription	Pancreas	Pancrea
47	chr11:71215800-71218400	Weak transcription	Thymus	Thymus
48	chr11:71215800-71219000	Weak transcription	Fetal Muscle Leg	muscle
49	chr11:71215800-71219400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr11:71216000-71217800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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