Variant report

Variant	rs12277408
Chromosome Location	chr11:71212219-71212220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr11:71211382-71212304	MCF-7	breast:	n/a	n/a
2	NR2F2	chr11:71211445-71212224	MCF-7	breast:	n/a	n/a
3	SIN3AK20	chr11:71211403-71212280	MCF-7	breast:	n/a	n/a
4	EP300	chr11:71211553-71212225	MCF-7	breast:	n/a	n/a
5	POLR2A	chr11:71212040-71212245	K562	blood:	n/a	n/a
6	TCF12	chr11:71211291-71212383	MCF-7	breast:	n/a	chr11:71211795-71211805
7	EP300	chr11:71211383-71212552	SK-N-SH	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:71210029..71213708-chr11:71213873..71217585,6	MCF-7	breast:
2	chr11:71212078..71213595-chr11:71215421..71217314,2	K562	blood:
3	chr11:71162728..71165710-chr11:71209612..71212447,2	K562	blood:
4	chr11:71205951..71209347-chr11:71211780..71215363,4	MCF-7	breast:
5	chr11:71192234..71193164-chr11:71211678..71212297,4	MCF-7	breast:

No data

Variant related genes	Relation type
NADSYN1	TF binding region
ENSG00000172893	Chromatin interaction
ENSG00000254924	Chromatin interaction
ENSG00000172890	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1002171	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]
rs11233868	0.90[EUR][1000 genomes]
rs11233947	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11501814	0.86[EUR][1000 genomes]
rs12273154	0.90[EUR][1000 genomes]
rs12275121	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12275635	0.90[EUR][1000 genomes]
rs12275636	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12283114	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12283177	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12283185	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12286569	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12286616	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12288906	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12289036	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12289074	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12289358	0.85[EUR][1000 genomes]
rs12574206	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12574554	0.90[EUR][1000 genomes]
rs12575605	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12575622	0.94[EUR][1000 genomes]
rs12576621	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12577807	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17161576	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17161578	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1893058	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2298776	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs28722015	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28823295	0.90[EUR][1000 genomes]
rs28898287	0.90[EUR][1000 genomes]
rs3794062	0.90[EUR][1000 genomes]
rs3794064	0.90[EUR][1000 genomes]
rs3814733	0.90[EUR][1000 genomes]
rs4316537	1.00[CEU][hapmap]
rs57017893	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57197278	0.90[EUR][1000 genomes]
rs57500217	0.90[EUR][1000 genomes]
rs57557229	0.90[EUR][1000 genomes]
rs57718633	0.88[EUR][1000 genomes]
rs58615796	0.94[EUR][1000 genomes]
rs59379414	0.90[EUR][1000 genomes]
rs59422671	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59487812	0.90[EUR][1000 genomes]
rs59511885	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59972361	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114525	0.90[EUR][1000 genomes]
rs7120978	0.90[EUR][1000 genomes]
rs7121106	0.90[EUR][1000 genomes]
rs7122671	1.00[CEU][hapmap]
rs7129044	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7130479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7483469	0.81[EUR][1000 genomes]
rs753352	0.88[EUR][1000 genomes]
rs7940351	0.88[EUR][1000 genomes]
rs7943296	0.88[EUR][1000 genomes]
rs7952035	1.00[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
6	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
7	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
8	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
rs12277408	NADSYN1	cis	Artery Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

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	chr11:71182200-71216000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:71182200-71216200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr11:71182200-71216200	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr11:71182200-71217800	Strong transcription	Primary T cells from cord blood	blood
9	chr11:71182400-71213800	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr11:71182400-71217200	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:71182400-71217600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr11:71182400-71217800	Strong transcription	Duodenum Mucosa	Duodenum
13	chr11:71182600-71213600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:71182800-71216400	Strong transcription	Stomach Smooth Muscle	stomach
15	chr11:71183000-71213400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr11:71189800-71218400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr11:71199400-71214600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:71199400-71215600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr11:71199600-71213000	Strong transcription	Primary B cells from cord blood	blood
20	chr11:71199600-71216400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:71199600-71218400	Strong transcription	Fetal Intestine Small	intestine
22	chr11:71200000-71215000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:71200000-71216000	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr11:71200200-71213200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr11:71200200-71216000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr11:71200200-71216400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr11:71200200-71217400	Strong transcription	Fetal Intestine Large	intestine
28	chr11:71200400-71213200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:71200400-71213800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr11:71200400-71216200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr11:71200400-71216400	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:71200600-71213200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr11:71200800-71215400	Strong transcription	Placenta	Placenta
34	chr11:71200800-71216800	Weak transcription	Fetal Kidney	kidney
35	chr11:71201000-71214600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:71201000-71215200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr11:71201000-71216200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:71201200-71212600	Strong transcription	GM12878-XiMat	blood
39	chr11:71201200-71213000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:71201200-71215400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr11:71201800-71216400	Strong transcription	Ovary	ovary
42	chr11:71203200-71215200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr11:71203400-71216800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr11:71205000-71213200	Strong transcription	Brain Angular Gyrus	brain
45	chr11:71205000-71214600	Strong transcription	Esophagus	oesophagus
46	chr11:71205200-71213000	Strong transcription	Brain Anterior Caudate	brain
47	chr11:71205200-71213000	Strong transcription	Rectal Smooth Muscle	rectum
48	chr11:71205200-71213400	Strong transcription	HepG2	liver
49	chr11:71205200-71215600	Strong transcription	Colonic Mucosa	Colon
50	chr11:71205200-71215600	Strong transcription	Duodenum Smooth Muscle	Duodenum

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