Variant report

Variant	rs11233933
Chromosome Location	chr11:71210070-71210071
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:71210018-71210536	HL-60	blood:	n/a	n/a
2	POLR2A	chr11:71209979-71210553	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:71210029..71213708-chr11:71213873..71217585,6	MCF-7	breast:
2	chr11:71162728..71165710-chr11:71209612..71212447,2	K562	blood:
3	chr11:71209374..71211618-chr11:71213015..71214853,2	K562	blood:

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

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10898186	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10898191	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10898201	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10898203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10898211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10898228	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10898234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898241	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11233977	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11234027	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11234030	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11234042	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1790349	0.92[ASW][hapmap];0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1790375	0.84[ASW][hapmap]
rs1792239	0.84[YRI][hapmap]
rs1792240	0.84[YRI][hapmap]
rs28762388	0.81[EUR][1000 genomes]
rs3829251	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7103591	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7114252	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7120029	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7130829	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7949129	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	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
8	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
9	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11233933	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs11233933	RP11-660L16.2	cis	Nerve Tibial	GTEx
rs11233933	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx
rs11233933	FOLR3	cis	parietal	SCAN
rs11233933	NADSYN1	cis	Nerve Tibial	GTEx
rs11233933	KRTAP5-9	cis	parietal	SCAN
rs11233933	RP11-660L16.2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:124 , 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	chr11:71182200-71211000	Strong transcription	Liver	Liver
6	chr11:71182200-71216000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:71182200-71216200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:71182200-71216200	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr11:71182200-71217800	Strong transcription	Primary T cells from cord blood	blood
10	chr11:71182400-71213800	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr11:71182400-71217200	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr11:71182400-71217600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:71182400-71217800	Strong transcription	Duodenum Mucosa	Duodenum
14	chr11:71182600-71210200	Strong transcription	Thymus	Thymus
15	chr11:71182600-71213600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr11:71182800-71216400	Strong transcription	Stomach Smooth Muscle	stomach
17	chr11:71183000-71213400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:71189800-71218400	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr11:71197800-71211800	Weak transcription	Fetal Brain Male	brain
20	chr11:71198800-71211400	Strong transcription	Adipose Nuclei	Adipose
21	chr11:71199200-71211200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr11:71199200-71211200	Strong transcription	Gastric	stomach
23	chr11:71199400-71214600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr11:71199400-71215600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr11:71199600-71213000	Strong transcription	Primary B cells from cord blood	blood
26	chr11:71199600-71216400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:71199600-71218400	Strong transcription	Fetal Intestine Small	intestine
28	chr11:71200000-71215000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:71200000-71216000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr11:71200200-71211200	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr11:71200200-71213200	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr11:71200200-71216000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr11:71200200-71216400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr11:71200200-71217400	Strong transcription	Fetal Intestine Large	intestine
35	chr11:71200400-71210200	Weak transcription	Fetal Heart	heart
36	chr11:71200400-71213200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr11:71200400-71213800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr11:71200400-71216200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr11:71200400-71216400	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr11:71200600-71213200	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr11:71200800-71215400	Strong transcription	Placenta	Placenta
42	chr11:71200800-71216800	Weak transcription	Fetal Kidney	kidney
43	chr11:71201000-71210200	Strong transcription	Fetal Muscle Trunk	muscle
44	chr11:71201000-71212000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:71201000-71214600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:71201000-71215200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr11:71201000-71216200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:71201200-71210200	Strong transcription	Fetal Muscle Leg	muscle
49	chr11:71201200-71212600	Strong transcription	GM12878-XiMat	blood
50	chr11:71201200-71213000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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