Variant report

Variant	rs11080640
Chromosome Location	chr18:13274118-13274119
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:13263986..13266782-chr18:13271778..13275109,3	MCF-7	breast:
2	chr18:13269904..13272111-chr18:13272211..13274676,2	MCF-7	breast:
3	chr18:13268397..13272481-chr18:13273229..13276163,4	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10775420	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10853230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11080639	0.83[MEX][hapmap];0.86[MKK][hapmap]
rs11080641	0.90[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11662800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12457309	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28563139	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4796974	0.82[TSI][hapmap]
rs56078702	0.90[ASN][1000 genomes]
rs7228720	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7232054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8093127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909408	chr18:13122618-13308950	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv909410	chr18:13151544-13308950	Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11080640	CR2	trans	lymphoblastoid	seeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13243600-13278200	Weak transcription	Dnd41	blood
2	chr18:13259200-13280000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr18:13261200-13282200	Weak transcription	Small Intestine	intestine
4	chr18:13267200-13276000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr18:13268400-13276800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr18:13268600-13276600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr18:13269400-13280000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr18:13269600-13274400	Enhancers	Right Ventricle	heart
9	chr18:13269600-13274600	Enhancers	Left Ventricle	heart
10	chr18:13270000-13274600	Enhancers	HepG2	liver
11	chr18:13270000-13276600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr18:13270000-13276800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr18:13270000-13279200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr18:13270000-13279800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr18:13270000-13283800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr18:13270000-13290000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr18:13270200-13278400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr18:13270200-13284600	Weak transcription	Psoas Muscle	Psoas
19	chr18:13270200-13288200	Weak transcription	Fetal Intestine Large	intestine
20	chr18:13270200-13290200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr18:13270200-13297600	Weak transcription	Colonic Mucosa	Colon
22	chr18:13270400-13279600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr18:13270600-13274200	Weak transcription	Brain Substantia Nigra	brain
24	chr18:13270800-13274600	Enhancers	Stomach Smooth Muscle	stomach
25	chr18:13270800-13279000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr18:13270800-13279800	Weak transcription	Adipose Nuclei	Adipose
27	chr18:13270800-13282600	Weak transcription	Fetal Intestine Small	intestine
28	chr18:13271400-13281600	Weak transcription	Brain Germinal Matrix	brain
29	chr18:13271800-13276600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr18:13271800-13278600	Weak transcription	Liver	Liver
31	chr18:13272600-13274400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr18:13272800-13274600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr18:13272800-13276400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr18:13272800-13276400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr18:13272800-13284800	Weak transcription	Esophagus	oesophagus
36	chr18:13272800-13289600	Weak transcription	Gastric	stomach
37	chr18:13273000-13274200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr18:13273000-13274200	Weak transcription	Brain Anterior Caudate	brain
39	chr18:13273000-13274400	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr18:13273000-13276400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr18:13273200-13274600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr18:13273200-13274600	Enhancers	Fetal Muscle Leg	muscle
43	chr18:13273200-13275400	Enhancers	Fetal Heart	heart
44	chr18:13273200-13276400	Weak transcription	Fetal Lung	lung
45	chr18:13273200-13283800	Weak transcription	Spleen	Spleen
46	chr18:13273400-13274400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr18:13273400-13274400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr18:13273400-13274600	Enhancers	Thymus	Thymus
49	chr18:13273600-13274200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr18:13273600-13274400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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