Variant report

Variant	rs7604404
Chromosome Location	chr2:173308318-173308319
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173290118..173293854-chr2:173304445..173308429,5	MCF-7	breast:
2	chr2:173297263..173301573-chr2:173305902..173308346,3	MCF-7	breast:
3	chr2:173305610..173308515-chr2:173310023..173312671,2	MCF-7	breast:
4	chr2:173307073..173308885-chr2:173311042..173312605,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DLX2-9	chr2:173308269-173308435	ucscGeneNc_uc002uht_1

Variant related genes	Relation type
ENSG00000226963	Chromatin interaction
ENSG00000091409	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10803874	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs12616959	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12620581	0.82[CEU][hapmap]
rs16860497	0.82[CEU][hapmap]
rs3792254	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs58514604	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7584971	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7584977	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7596259	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7608097	0.80[ASN][1000 genomes]
rs9287954	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv1847874	chr2:173277361-173308318	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7604404	KLHL23	cis	parietal	SCAN
rs7604404	GAD1	cis	cerebellum	SCAN
rs7604404	CHRNA1	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173294800-173308800	Enhancers	Stomach Mucosa	stomach
2	chr2:173295600-173308600	Enhancers	Fetal Intestine Large	intestine
3	chr2:173296600-173308600	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr2:173301000-173308400	Enhancers	Fetal Intestine Small	intestine
5	chr2:173301200-173308400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr2:173301400-173308400	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr2:173303200-173308400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:173303200-173309600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:173304200-173311400	Weak transcription	Liver	Liver
10	chr2:173304600-173308400	Enhancers	HSMM	muscle
11	chr2:173304600-173308800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:173304600-173310400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:173304800-173308800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:173305000-173310400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:173305000-173316800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:173305400-173309000	Enhancers	Fetal Muscle Leg	muscle
17	chr2:173305800-173308800	Enhancers	Fetal Heart	heart
18	chr2:173306000-173308400	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:173306200-173310400	Weak transcription	Fetal Lung	lung
20	chr2:173306200-173311200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:173306800-173309800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:173306800-173311400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr2:173306800-173316400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:173307000-173308400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr2:173307000-173308600	Enhancers	Primary T cells fromperipheralblood	blood
26	chr2:173307000-173308600	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr2:173307000-173308600	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr2:173307000-173309600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr2:173307000-173309600	Weak transcription	Brain Germinal Matrix	brain
30	chr2:173307000-173310600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:173307200-173308400	Enhancers	HSMMtube	muscle
32	chr2:173307200-173318600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:173307400-173308400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:173307400-173308400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:173307400-173310400	Weak transcription	Brain Substantia Nigra	brain
36	chr2:173307400-173310400	Weak transcription	Gastric	stomach
37	chr2:173307400-173310400	Weak transcription	Spleen	Spleen
38	chr2:173307400-173310400	Weak transcription	NHLF	lung
39	chr2:173307400-173310600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:173307400-173312800	Weak transcription	Fetal Kidney	kidney
41	chr2:173307400-173313600	Weak transcription	Placenta	Placenta
42	chr2:173307400-173322400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr2:173307600-173308400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:173307600-173308400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr2:173307600-173308400	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr2:173307600-173308600	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr2:173307600-173308800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:173307600-173309000	Enhancers	A549	lung
49	chr2:173307600-173309200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:173307600-173310200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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