Variant report

Variant	rs7943296
Chromosome Location	chr11:71194199-71194200
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:71156994..71165841-chr11:71185066..71202614,31	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172893	Chromatin interaction
ENSG00000172890	Chromatin interaction
ENSG00000254682	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1002171	0.83[EUR][1000 genomes]
rs11233868	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11233947	0.88[EUR][1000 genomes]
rs11501814	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12273154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12275635	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12275636	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12277408	0.88[EUR][1000 genomes]
rs12283114	0.85[EUR][1000 genomes]
rs12283177	0.85[EUR][1000 genomes]
rs12283185	0.85[EUR][1000 genomes]
rs12286569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12286616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12288906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12289036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12289074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12289358	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12574206	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12574554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12575605	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12575622	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12576621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12577807	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161578	0.88[EUR][1000 genomes]
rs1893058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2298776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28722015	0.96[EUR][1000 genomes]
rs28823295	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28898287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794062	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3794064	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3814733	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4316537	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs57017893	0.88[EUR][1000 genomes]
rs57197278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57500217	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57557229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57718633	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58615796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59379414	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59422671	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59487812	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59511885	0.83[EUR][1000 genomes]
rs59972361	0.88[EUR][1000 genomes]
rs7114525	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7120978	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7121106	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7129044	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7130479	0.92[EUR][1000 genomes]
rs753352	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940351	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv526973	chr11:71088949-71215880	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv897898	chr11:71103143-71211654	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv519224	chr11:71108341-71215880	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1037357	chr11:71162241-71209628	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
8	nsv541085	chr11:71162241-71209628	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1052432	chr11:71167449-71213007	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7943296	NADSYN1	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71165000-71210000	Weak transcription	Psoas Muscle	Psoas
2	chr11:71165200-71199200	Weak transcription	Right Atrium	heart
3	chr11:71165400-71194200	Weak transcription	Fetal Heart	heart
4	chr11:71165800-71218400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr11:71166000-71194200	Weak transcription	Fetal Brain Male	brain
6	chr11:71172200-71195000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:71180600-71199000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:71180800-71197600	Strong transcription	Fetal Intestine Small	intestine
9	chr11:71180800-71198400	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr11:71180800-71199400	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr11:71181400-71217800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr11:71181800-71218000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr11:71182000-71197600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr11:71182000-71197800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr11:71182000-71198400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr11:71182000-71198800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr11:71182000-71217600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:71182200-71195800	Strong transcription	Lung	lung
19	chr11:71182200-71197800	Strong transcription	Brain Cingulate Gyrus	brain
20	chr11:71182200-71197800	Strong transcription	Brain Inferior Temporal Lobe	brain
21	chr11:71182200-71198000	Strong transcription	Brain Hippocampus Middle	brain
22	chr11:71182200-71198400	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr11:71182200-71198400	Strong transcription	Brain Anterior Caudate	brain
24	chr11:71182200-71198600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr11:71182200-71198600	Strong transcription	Fetal Muscle Leg	muscle
26	chr11:71182200-71198600	Strong transcription	Fetal Stomach	stomach
27	chr11:71182200-71211000	Strong transcription	Liver	Liver
28	chr11:71182200-71216000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr11:71182200-71216200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr11:71182200-71216200	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr11:71182200-71217800	Strong transcription	Primary T cells from cord blood	blood
32	chr11:71182400-71197000	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr11:71182400-71197600	Strong transcription	Colonic Mucosa	Colon
34	chr11:71182400-71197800	Strong transcription	Primary B cells from cord blood	blood
35	chr11:71182400-71197800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:71182400-71197800	Strong transcription	Aorta	Aorta
37	chr11:71182400-71197800	Strong transcription	Brain Angular Gyrus	brain
38	chr11:71182400-71197800	Strong transcription	Fetal Brain Female	brain
39	chr11:71182400-71197800	Strong transcription	Fetal Intestine Large	intestine
40	chr11:71182400-71197800	Strong transcription	Rectal Smooth Muscle	rectum
41	chr11:71182400-71198200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr11:71182400-71198200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:71182400-71198400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr11:71182400-71198400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr11:71182400-71198400	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr11:71182400-71198800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr11:71182400-71198800	Strong transcription	GM12878-XiMat	blood
48	chr11:71182400-71199000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr11:71182400-71199600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr11:71182400-71199800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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