Variant report

Variant	rs7120029
Chromosome Location	chr11:71198957-71198958
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

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

No data

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

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10898186	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10898191	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10898193	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10898201	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10898203	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10898211	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10898223	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10898228	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10898234	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898241	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11233933	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11233977	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11234027	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11234030	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11234042	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1790349	0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs3829251	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7103591	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7114252	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7130829	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7949129	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7120029	RP11-660L16.2	cis	Heart Left Ventricle	GTEx
rs7120029	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7120029	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs7120029	RP11-660L16.2	cis	Thyroid	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	chr11:71165800-71218400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr11:71180600-71199000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:71180800-71199400	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr11:71181400-71217800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr11:71181800-71218000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr11:71182000-71217600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:71182200-71211000	Strong transcription	Liver	Liver
10	chr11:71182200-71216000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr11:71182200-71216200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:71182200-71216200	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr11:71182200-71217800	Strong transcription	Primary T cells from cord blood	blood
14	chr11:71182400-71199000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr11:71182400-71199600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr11:71182400-71199800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr11:71182400-71213800	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr11:71182400-71217200	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:71182400-71217600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:71182400-71217800	Strong transcription	Duodenum Mucosa	Duodenum
21	chr11:71182600-71204000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr11:71182600-71210200	Strong transcription	Thymus	Thymus
23	chr11:71182600-71213600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr11:71182800-71216400	Strong transcription	Stomach Smooth Muscle	stomach
25	chr11:71183000-71199600	Strong transcription	Dnd41	blood
26	chr11:71183000-71213400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr11:71189800-71218400	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr11:71190000-71199000	Strong transcription	Spleen	Spleen
29	chr11:71195200-71203000	Weak transcription	Stomach Mucosa	stomach
30	chr11:71195400-71199000	Weak transcription	K562	blood
31	chr11:71195400-71204400	Weak transcription	Hela-S3	cervix
32	chr11:71195400-71206000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr11:71195600-71201200	Weak transcription	Small Intestine	intestine
34	chr11:71195600-71208000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr11:71195800-71199000	Weak transcription	HMEC	breast
36	chr11:71196000-71199000	Weak transcription	Fetal Heart	heart
37	chr11:71196200-71199400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:71196200-71200200	Weak transcription	Fetal Kidney	kidney
39	chr11:71196200-71209600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr11:71196400-71207600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr11:71196800-71199000	Weak transcription	HepG2	liver
42	chr11:71197000-71200800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr11:71197000-71201800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr11:71197000-71202000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr11:71197400-71199800	Weak transcription	Brain Germinal Matrix	brain
46	chr11:71197400-71205200	Weak transcription	Colon Smooth Muscle	Colon
47	chr11:71197600-71199000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr11:71197600-71199000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr11:71197600-71199000	Weak transcription	Fetal Intestine Small	intestine
50	chr11:71197600-71199000	Weak transcription	Osteobl	bone

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