Variant report

Variant	rs504141
Chromosome Location	chr7:100309125-100309126
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:100269447..100271845-chr7:100308979..100311656,2	K562	blood:
2	chr7:100304410..100307570-chr7:100307942..100309622,3	MCF-7	breast:
3	chr7:100305178..100307806-chr7:100309002..100310752,2	K562	blood:
4	chr7:100308383..100310094-chr7:100311797..100313308,2	MCF-7	breast:
5	chr7:100302997..100306317-chr7:100307854..100311293,5	K562	blood:
6	chr7:100301507..100303500-chr7:100307658..100310486,2	MCF-7	breast:
7	chr7:100302099..100306340-chr7:100306369..100309524,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172336	Chromatin interaction
ENSG00000172354	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10277087	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[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];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10953301	0.89[JPT][hapmap]
rs11520986	0.89[JPT][hapmap]
rs11974395	0.89[JPT][hapmap]
rs11979818	0.89[JPT][hapmap]
rs11983334	0.89[JPT][hapmap]
rs1617640	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1734908	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1734909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1734910	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075672	0.82[MEX][hapmap]
rs221771	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs221772	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs221788	0.87[EUR][1000 genomes]
rs221790	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs221795	1.00[ASW][hapmap];0.84[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs221801	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[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];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2272572	0.89[JPT][hapmap]
rs2432930	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4727459	0.89[JPT][hapmap]
rs4729597	0.83[MEX][hapmap]
rs4729602	0.89[JPT][hapmap]
rs4729606	0.89[JPT][hapmap]
rs4729607	0.89[JPT][hapmap]
rs475339	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs507392	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs551238	0.94[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs554055	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs568733	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576236	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
3	nsv888785	chr7:100141861-100313420	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv888786	chr7:100159567-100313420	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv831072	chr7:100162503-100362835	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv888791	chr7:100221867-100371114	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv607933	chr7:100240191-100365613	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv470381	chr7:100240191-100431980	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv8184	chr7:100240737-100345945	Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	nsv888792	chr7:100252918-100329189	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	esv1804951	chr7:100275135-100374093	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs504141	TAC1	cis	parietal	SCAN
rs504141	DLX5	cis	cerebellum	SCAN
rs504141	PILRB	cis	cerebellum	SCAN
rs504141	POLR2J	cis	parietal	SCAN
rs504141	TSC22D4	cis	parietal	SCAN
rs504141	C10orf107	trans	parietal	SCAN
rs504141	MOSPD3	cis	Whole Blood	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100305000-100309200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr7:100305000-100309800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr7:100305000-100318000	Weak transcription	Right Atrium	heart
4	chr7:100305200-100309200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr7:100305200-100309200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr7:100305200-100310000	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr7:100305200-100310200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:100305200-100310400	Weak transcription	Brain Anterior Caudate	brain
9	chr7:100305200-100311000	Weak transcription	Fetal Intestine Large	intestine
10	chr7:100305200-100311800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr7:100305200-100313200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:100305200-100313400	Weak transcription	Brain Germinal Matrix	brain
13	chr7:100305200-100315000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr7:100305200-100318400	Weak transcription	Gastric	stomach
15	chr7:100305400-100309200	Weak transcription	Brain Hippocampus Middle	brain
16	chr7:100305400-100309200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr7:100305400-100309400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr7:100305400-100309400	Weak transcription	A549	lung
19	chr7:100305400-100309400	Weak transcription	NHLF	lung
20	chr7:100305400-100309600	Enhancers	Liver	Liver
21	chr7:100305400-100311400	Weak transcription	Brain Angular Gyrus	brain
22	chr7:100305400-100313000	Weak transcription	NH-A	brain
23	chr7:100305600-100312200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr7:100305800-100309600	Weak transcription	Hela-S3	cervix
25	chr7:100306000-100309400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr7:100306000-100309400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:100306000-100310000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:100306000-100310000	Weak transcription	HSMM	muscle
29	chr7:100306000-100313200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:100306200-100310000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr7:100306200-100314400	Weak transcription	Lung	lung
32	chr7:100306400-100309200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr7:100306400-100309200	Weak transcription	NHEK	skin
34	chr7:100306400-100311000	Weak transcription	K562	blood
35	chr7:100306400-100313200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr7:100306600-100311600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr7:100306800-100309200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr7:100306800-100309600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr7:100306800-100309800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr7:100306800-100312400	Weak transcription	Primary T cells from cord blood	blood
41	chr7:100306800-100312400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr7:100306800-100312400	Weak transcription	Fetal Muscle Leg	muscle
43	chr7:100306800-100315400	Weak transcription	Placenta	Placenta
44	chr7:100306800-100315600	Weak transcription	HepG2	liver
45	chr7:100307000-100309800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr7:100307000-100310200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr7:100307000-100310400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr7:100307000-100311400	Weak transcription	Fetal Intestine Small	intestine
49	chr7:100307400-100310200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr7:100307800-100311600	Weak transcription	Fetal Stomach	stomach

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