Variant report

Variant	rs11140229
Chromosome Location	chr9:86351976-86351977
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86320830..86324231-chr9:86351676..86355112,3	MCF-7	breast:
2	chr9:86350659..86352740-chr9:86367582..86369974,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135018	Chromatin interaction
ENSG00000254473	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11140178	0.85[EUR][1000 genomes]
rs11140179	1.00[EUR][1000 genomes]
rs11140182	1.00[EUR][1000 genomes]
rs11140183	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11140191	1.00[EUR][1000 genomes]
rs11140192	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11140197	0.86[EUR][1000 genomes]
rs11140199	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11140203	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11140215	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11140217	1.00[EUR][1000 genomes]
rs11140219	1.00[EUR][1000 genomes]
rs11140225	1.00[EUR][1000 genomes]
rs11140228	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140230	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140235	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11140248	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140250	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140252	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140257	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140258	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140266	0.92[EUR][1000 genomes]
rs11140269	0.85[EUR][1000 genomes]
rs11140270	0.85[EUR][1000 genomes]
rs11140280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11140288	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11140291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11140294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11559387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11560627	1.00[EUR][1000 genomes]
rs12235151	0.92[EUR][1000 genomes]
rs12235969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12236455	0.92[EUR][1000 genomes]
rs12236743	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12237262	1.00[EUR][1000 genomes]
rs12237555	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12238365	1.00[EUR][1000 genomes]
rs12238575	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2282221	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2282222	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs28627139	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655802	0.86[EUR][1000 genomes]
rs3763626	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv893513	chr9:86298632-86433459	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv973432	chr9:86330626-86371524	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86347400-86354200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:86347800-86366200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr9:86348400-86415400	Weak transcription	Fetal Heart	heart
4	chr9:86350000-86431600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:86350200-86374600	Weak transcription	Fetal Muscle Leg	muscle
6	chr9:86350600-86352400	Weak transcription	Primary T cells from cord blood	blood
7	chr9:86350600-86352800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:86350800-86352200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr9:86350800-86352400	Weak transcription	Left Ventricle	heart
10	chr9:86350800-86407000	Weak transcription	Primary B cells from cord blood	blood
11	chr9:86351000-86367000	Weak transcription	Fetal Intestine Small	intestine
12	chr9:86351000-86367000	Weak transcription	Fetal Stomach	stomach
13	chr9:86351000-86393200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr9:86351200-86358600	Weak transcription	Psoas Muscle	Psoas
15	chr9:86351200-86366000	Weak transcription	Brain Hippocampus Middle	brain
16	chr9:86351400-86353200	Weak transcription	Adipose Nuclei	Adipose
17	chr9:86351400-86366800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:86351400-86367000	Weak transcription	Thymus	Thymus
19	chr9:86351400-86371000	Weak transcription	Colon Smooth Muscle	Colon
20	chr9:86351600-86352800	Weak transcription	Liver	Liver

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