Variant report

Variant	rs2394824
Chromosome Location	chr7:97739317-97739318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:97738785..97741480-chr7:97751864..97754009,2	MCF-7	breast:
2	chr7:97733859..97737866-chr7:97738343..97741740,8	K562	blood:
3	chr7:97737823..97740365-chr7:97743059..97746026,2	K562	blood:
4	chr7:97737313..97739536-chr7:97747241..97749393,2	K562	blood:

Variant related genes	Relation type
ENSG00000164715	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1039057	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11761896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11762771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11762810	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11768678	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11772060	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11773169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1532380	0.96[EUR][1000 genomes]
rs17169325	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4729404	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4729408	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55761857	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55765204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56006208	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56034325	0.95[EUR][1000 genomes]
rs56088922	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56174823	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56389625	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58911561	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62479768	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62479773	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62479795	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62479797	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73149199	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs740208	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs884897	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats 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
8	esv1816676	chr7:97676259-97868033	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv831066	chr7:97726879-97890550	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2394824	DKFZP434B0335	Cis_1M	lymphoblastoid	RTeQTL
rs2394824	FIS1	cis	parietal	SCAN
rs2394824	TECPR1	cis	parietal	SCAN
rs2394824	BAIAP2L1	cis	cerebellum	SCAN
rs2394824	AKAP8	trans	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97737000-97745200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:97737000-97746200	Weak transcription	Spleen	Spleen
3	chr7:97737200-97741800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:97737200-97741800	Weak transcription	Lung	lung
5	chr7:97737200-97745600	Weak transcription	Gastric	stomach
6	chr7:97737200-97746200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr7:97737200-97762400	Weak transcription	Aorta	Aorta
8	chr7:97737200-97764600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr7:97737400-97739400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr7:97737400-97741800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr7:97737400-97743400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr7:97737400-97744400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr7:97737600-97739600	Weak transcription	Brain Germinal Matrix	brain
14	chr7:97737600-97739800	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr7:97737600-97740800	Weak transcription	Pancreas	Pancrea
16	chr7:97737600-97741400	Enhancers	Fetal Intestine Large	intestine
17	chr7:97737600-97741600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr7:97737600-97754400	Weak transcription	HSMMtube	muscle
19	chr7:97737600-97762400	Weak transcription	Small Intestine	intestine
20	chr7:97737800-97739400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr7:97737800-97739400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr7:97737800-97739600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:97737800-97739600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:97737800-97739800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr7:97737800-97740400	Weak transcription	Psoas Muscle	Psoas
26	chr7:97737800-97741000	Enhancers	Fetal Intestine Small	intestine
27	chr7:97737800-97741200	Enhancers	Fetal Brain Male	brain
28	chr7:97737800-97743600	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr7:97737800-97745600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:97737800-97748600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr7:97737800-97749400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr7:97737800-97751000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr7:97737800-97759600	Weak transcription	Right Ventricle	heart
34	chr7:97737800-97760800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr7:97737800-97767000	Weak transcription	Fetal Stomach	stomach
36	chr7:97738000-97739400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr7:97738000-97739400	Enhancers	A549	lung
38	chr7:97738000-97739600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr7:97738000-97739600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr7:97738000-97739600	Weak transcription	Adipose Nuclei	Adipose
41	chr7:97738000-97739600	Weak transcription	Brain Angular Gyrus	brain
42	chr7:97738000-97739800	Weak transcription	Right Atrium	heart
43	chr7:97738000-97740600	Weak transcription	Stomach Mucosa	stomach
44	chr7:97738000-97743000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:97738000-97746200	Weak transcription	NHEK	skin
46	chr7:97738000-97748400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr7:97738000-97748400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr7:97738000-97751600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr7:97738200-97739400	Weak transcription	Fetal Heart	heart
50	chr7:97738200-97739600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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