Variant report

Variant	rs28627139
Chromosome Location	chr9:86413279-86413280
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86411947..86414043-chr9:86595098..86597695,2	MCF-7	breast:
2	chr9:86402003..86404732-chr9:86411861..86414651,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178966	Chromatin interaction
ENSG00000165119	Chromatin interaction
ENSG00000165113	Chromatin interaction

Extended variants
information (count: 43 )
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]
rs11140250	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]
rs28655802	0.86[EUR][1000 genomes]
rs3763626	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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:83 , 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	chr9:86353000-86432000	Weak transcription	Lung	lung
4	chr9:86363800-86431200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr9:86364800-86413400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr9:86367000-86413600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr9:86377200-86432000	Weak transcription	Gastric	stomach
8	chr9:86378400-86418400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr9:86380200-86431600	Weak transcription	Fetal Kidney	kidney
10	chr9:86383600-86425800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr9:86389000-86431600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:86392000-86431600	Weak transcription	Psoas Muscle	Psoas
13	chr9:86392000-86431800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:86394400-86431600	Weak transcription	Colon Smooth Muscle	Colon
15	chr9:86395000-86416400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr9:86395600-86417400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:86397000-86420000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr9:86397400-86413400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr9:86397400-86415600	Weak transcription	Brain Germinal Matrix	brain
20	chr9:86397400-86419400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr9:86397400-86423400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr9:86399000-86431000	Weak transcription	A549	lung
23	chr9:86399400-86431000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:86399400-86431200	Weak transcription	Fetal Stomach	stomach
25	chr9:86399400-86431400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr9:86399400-86431600	Weak transcription	Right Ventricle	heart
27	chr9:86399400-86431800	Weak transcription	Esophagus	oesophagus
28	chr9:86399400-86431800	Weak transcription	Pancreas	Pancrea
29	chr9:86402800-86431600	Weak transcription	Fetal Brain Female	brain
30	chr9:86406800-86422200	Weak transcription	Spleen	Spleen
31	chr9:86407000-86431600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:86407800-86420600	Weak transcription	Primary B cells from cord blood	blood
33	chr9:86408200-86415400	Weak transcription	Hela-S3	cervix
34	chr9:86408200-86431200	Weak transcription	Dnd41	blood
35	chr9:86409000-86414200	Strong transcription	Fetal Thymus	thymus
36	chr9:86409200-86413400	Weak transcription	Fetal Intestine Small	intestine
37	chr9:86409400-86415800	Weak transcription	GM12878-XiMat	blood
38	chr9:86409400-86415800	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr9:86409600-86420600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr9:86409800-86431600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:86410000-86423200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr9:86410400-86432000	Weak transcription	Small Intestine	intestine
43	chr9:86411000-86413400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr9:86411200-86431400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr9:86411400-86413800	Strong transcription	Fetal Muscle Trunk	muscle
46	chr9:86411400-86416200	Strong transcription	Liver	Liver
47	chr9:86411600-86414400	Weak transcription	Fetal Brain Male	brain
48	chr9:86411600-86414800	Strong transcription	Fetal Intestine Large	intestine
49	chr9:86411800-86413400	Strong transcription	Brain Substantia Nigra	brain
50	chr9:86411800-86413800	Strong transcription	Brain Hippocampus Middle	brain

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