Variant report

Variant	rs12576621
Chromosome Location	chr11:71199666-71199667
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:71199654..71202041-chr11:71202100..71204531,2	K562	blood:
2	chr11:71156994..71165841-chr11:71185066..71202614,31	MCF-7	breast:
3	chr11:71198500..71200702-chr11:71204795..71207728,3	MCF-7	breast:
4	chr11:71198072..71200599-chr11:71283906..71285709,2	MCF-7	breast:
5	chr11:71198148..71200436-chr11:71273726..71275977,2	MCF-7	breast:
6	chr11:71197542..71205760-chr11:71207868..71214040,12	MCF-7	breast:
7	chr11:71154436..71156970-chr11:71198755..71201662,2	MCF-7	breast:
8	chr11:71164126..71164763-chr11:71198880..71199776,2	MCF-7	breast:
9	chr11:71188326..71191003-chr11:71198229..71200768,2	K562	blood:
10	chr11:71197776..71200724-chr11:71214372..71216917,2	MCF-7	breast:

No data

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

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1002171	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs11233868	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11233947	0.90[EUR][1000 genomes]
rs11501814	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12273154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12275635	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12275636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12277408	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12283114	0.86[EUR][1000 genomes]
rs12283177	0.86[EUR][1000 genomes]
rs12283185	0.86[EUR][1000 genomes]
rs12286569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12286616	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12288906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12289036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12289074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12289358	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12574206	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12574554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12575605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12575622	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12577807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161578	0.90[EUR][1000 genomes]
rs1893058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2298776	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28722015	0.98[EUR][1000 genomes]
rs28823295	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28898287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794062	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3794064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3814733	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4316537	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs57017893	0.90[EUR][1000 genomes]
rs57197278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57500217	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57557229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57718633	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58615796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59379414	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59422671	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59487812	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59511885	0.84[EUR][1000 genomes]
rs59972361	0.90[EUR][1000 genomes]
rs7114525	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7120978	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7121106	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7122671	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap]
rs7129044	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7130479	0.94[EUR][1000 genomes]
rs753352	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940351	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952035	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12576621	NADSYN1	cis	lymphoblastoid	seeQTL
rs12576621	NADSYN1	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 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	chr11:71165800-71218400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr11:71181400-71217800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr11:71181800-71218000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr11:71182000-71217600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:71182200-71211000	Strong transcription	Liver	Liver
7	chr11:71182200-71216000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr11:71182200-71216200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr11:71182200-71216200	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr11:71182200-71217800	Strong transcription	Primary T cells from cord blood	blood
11	chr11:71182400-71199800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr11:71182400-71213800	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr11:71182400-71217200	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr11:71182400-71217600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:71182400-71217800	Strong transcription	Duodenum Mucosa	Duodenum
16	chr11:71182600-71204000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:71182600-71210200	Strong transcription	Thymus	Thymus
18	chr11:71182600-71213600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr11:71182800-71216400	Strong transcription	Stomach Smooth Muscle	stomach
20	chr11:71183000-71213400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:71189800-71218400	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr11:71195200-71203000	Weak transcription	Stomach Mucosa	stomach
23	chr11:71195400-71204400	Weak transcription	Hela-S3	cervix
24	chr11:71195400-71206000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr11:71195600-71201200	Weak transcription	Small Intestine	intestine
26	chr11:71195600-71208000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr11:71196200-71200200	Weak transcription	Fetal Kidney	kidney
28	chr11:71196200-71209600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr11:71196400-71207600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr11:71197000-71200800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr11:71197000-71201800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr11:71197000-71202000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr11:71197400-71199800	Weak transcription	Brain Germinal Matrix	brain
34	chr11:71197400-71205200	Weak transcription	Colon Smooth Muscle	Colon
35	chr11:71197600-71200400	Weak transcription	Right Ventricle	heart
36	chr11:71197600-71200800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr11:71197600-71200800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr11:71197600-71200800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr11:71197600-71202000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr11:71197600-71206400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr11:71197800-71200000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr11:71197800-71200000	Weak transcription	Esophagus	oesophagus
43	chr11:71197800-71200200	Weak transcription	Fetal Intestine Large	intestine
44	chr11:71197800-71200400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr11:71197800-71200600	Weak transcription	Aorta	Aorta
46	chr11:71197800-71200600	Weak transcription	Brain Angular Gyrus	brain
47	chr11:71197800-71200600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr11:71197800-71200600	Weak transcription	Fetal Thymus	thymus
49	chr11:71197800-71201200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr11:71197800-71201800	Weak transcription	Left Ventricle	heart

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