Variant report

Variant	rs11140250
Chromosome Location	chr9:86401778-86401779
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	chr9:86321345..86324567-chr9:86398481..86402531,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135018	Chromatin interaction
ENSG00000254473	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

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[EUR][1000 genomes]
rs11140191	1.00[EUR][1000 genomes]
rs11140192	1.00[EUR][1000 genomes]
rs11140197	0.86[EUR][1000 genomes]
rs11140199	1.00[EUR][1000 genomes]
rs11140203	1.00[EUR][1000 genomes]
rs11140215	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]
rs11140229	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]
rs11140248	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140252	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140254	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]
rs11559387	0.85[EUR][1000 genomes]
rs11560627	1.00[EUR][1000 genomes]
rs12235151	0.92[EUR][1000 genomes]
rs12236455	0.92[EUR][1000 genomes]
rs12236743	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[EUR][1000 genomes]
rs2282221	1.00[EUR][1000 genomes]
rs2282222	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:6 , 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	nsv973849	chr9:86394251-86402032	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
4	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv2761538	chr9:86401015-86451943	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86348400-86415400	Weak transcription	Fetal Heart	heart
2	chr9:86350000-86431600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr9:86350800-86407000	Weak transcription	Primary B cells from cord blood	blood
4	chr9:86352000-86411800	Weak transcription	Ovary	ovary
5	chr9:86353000-86432000	Weak transcription	Lung	lung
6	chr9:86363800-86412400	Weak transcription	HepG2	liver
7	chr9:86363800-86431200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr9:86364800-86412000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr9:86364800-86413400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr9:86367000-86413600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr9:86367400-86411800	Weak transcription	Brain Substantia Nigra	brain
12	chr9:86367600-86412000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr9:86373200-86411800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr9:86377000-86412600	Weak transcription	Brain Anterior Caudate	brain
15	chr9:86377200-86432000	Weak transcription	Gastric	stomach
16	chr9:86378400-86418400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr9:86380200-86431600	Weak transcription	Fetal Kidney	kidney
18	chr9:86381400-86411800	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:86383600-86425800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr9:86385400-86409200	Weak transcription	Primary T cells from cord blood	blood
21	chr9:86388200-86411400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr9:86389000-86431600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr9:86391800-86411800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr9:86392000-86431600	Weak transcription	Psoas Muscle	Psoas
25	chr9:86392000-86431800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:86393400-86412000	Weak transcription	Brain Angular Gyrus	brain
27	chr9:86393600-86412400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr9:86394400-86431600	Weak transcription	Colon Smooth Muscle	Colon
29	chr9:86394800-86412600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr9:86395000-86416400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr9:86395600-86417400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:86396600-86403400	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr9:86397000-86402400	Strong transcription	Liver	Liver
34	chr9:86397000-86420000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr9:86397400-86412200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr9:86397400-86413400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr9:86397400-86415600	Weak transcription	Brain Germinal Matrix	brain
38	chr9:86397400-86419400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr9:86397400-86423400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr9:86398600-86402200	Weak transcription	Fetal Brain Female	brain
41	chr9:86399000-86431000	Weak transcription	A549	lung
42	chr9:86399400-86408800	Weak transcription	Fetal Intestine Small	intestine
43	chr9:86399400-86408800	Weak transcription	Left Ventricle	heart
44	chr9:86399400-86409600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr9:86399400-86411400	Weak transcription	Aorta	Aorta
46	chr9:86399400-86411800	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr9:86399400-86412000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr9:86399400-86412200	Weak transcription	Fetal Muscle Leg	muscle
49	chr9:86399400-86412200	Weak transcription	Thymus	Thymus
50	chr9:86399400-86431000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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