Variant report

Variant	rs28654199
Chromosome Location	chr9:96024365-96024366
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:96020313..96022881-chr9:96023232..96025158,2	MCF-7	breast:
2	chr9:96022448..96025366-chr9:96049788..96053547,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165238	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10114908	0.84[AFR][1000 genomes]
rs10121188	0.95[AFR][1000 genomes]
rs12338028	1.00[AMR][1000 genomes]
rs12341311	0.91[AFR][1000 genomes]
rs16909013	0.90[AFR][1000 genomes]
rs7030881	1.00[AMR][1000 genomes]
rs73651203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7848480	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv893583	chr9:95996573-96091688	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv893584	chr9:96002983-96116937	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95995200-96026400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr9:95995600-96030600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:96005400-96033800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:96005600-96026200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:96006200-96043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:96008000-96030200	Strong transcription	Fetal Intestine Small	intestine
7	chr9:96008000-96030400	Strong transcription	Fetal Intestine Large	intestine
8	chr9:96008200-96026600	Weak transcription	Spleen	Spleen
9	chr9:96008200-96027600	Weak transcription	Right Atrium	heart
10	chr9:96008800-96026200	Weak transcription	Placenta	Placenta
11	chr9:96011000-96026400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:96011200-96030600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:96011200-96032800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:96011200-96033400	Weak transcription	A549	lung
15	chr9:96011800-96026200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr9:96012800-96032600	Weak transcription	Fetal Brain Male	brain
17	chr9:96013000-96031400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr9:96014000-96033800	Strong transcription	Stomach Smooth Muscle	stomach
19	chr9:96014400-96025400	Strong transcription	Brain Germinal Matrix	brain
20	chr9:96014400-96032800	Strong transcription	Fetal Brain Female	brain
21	chr9:96014800-96026800	Weak transcription	Fetal Heart	heart
22	chr9:96015400-96026600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr9:96015800-96026200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr9:96017400-96033200	Weak transcription	Brain Substantia Nigra	brain
25	chr9:96017800-96026400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr9:96017800-96030200	Weak transcription	Brain Angular Gyrus	brain
27	chr9:96018400-96033200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr9:96019200-96026600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr9:96019600-96024400	Weak transcription	HepG2	liver
30	chr9:96020000-96030000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr9:96020600-96029200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:96021000-96024600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr9:96022400-96026400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr9:96022600-96024800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr9:96022600-96030800	Enhancers	Fetal Thymus	thymus
36	chr9:96022800-96025400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr9:96023000-96024400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr9:96023000-96026000	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr9:96023000-96026400	Weak transcription	Brain Anterior Caudate	brain
40	chr9:96023200-96024800	Weak transcription	Fetal Muscle Leg	muscle
41	chr9:96023200-96025600	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr9:96023400-96025000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr9:96023400-96025800	Genic enhancers	Duodenum Mucosa	Duodenum
44	chr9:96023400-96025800	Enhancers	Stomach Mucosa	stomach
45	chr9:96023400-96026400	Weak transcription	Right Ventricle	heart
46	chr9:96023800-96025400	Weak transcription	Colon Smooth Muscle	Colon
47	chr9:96024000-96024400	Strong transcription	Colonic Mucosa	Colon
48	chr9:96024000-96025400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr9:96024000-96025400	Enhancers	Thymus	Thymus
50	chr9:96024000-96025600	Enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links