Variant report

Variant	rs1421604
Chromosome Location	chr7:138176538-138176539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:138174765-138177053	HepG2	liver:	n/a	n/a
2	NFYA	chr7:138176522-138176693	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:138175711-138176554	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000234995	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10155993	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10215281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10227693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10232771	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10247380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10248731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10258706	0.90[ASN][1000 genomes]
rs1030961	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1077772	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11976614	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12112459	0.90[ASN][1000 genomes]
rs12666310	0.80[ASN][1000 genomes]
rs1363053	0.94[CEU][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes]
rs1544733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1673203	0.94[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1673204	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap]
rs1673205	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1673206	0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs17364560	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs17461551	0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1813003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1874326	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.84[MEX][hapmap]
rs2353354	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2353355	0.83[ASN][1000 genomes]
rs3757381	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3778705	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs3807155	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3807156	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3807157	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs3816192	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55723768	0.93[ASN][1000 genomes]
rs56092804	0.93[ASN][1000 genomes]
rs57407834	0.93[ASN][1000 genomes]
rs58562866	0.90[ASN][1000 genomes]
rs62485263	0.81[ASN][1000 genomes]
rs62485264	0.81[ASN][1000 genomes]
rs62487613	0.80[ASN][1000 genomes]
rs62487615	0.90[ASN][1000 genomes]
rs62487616	0.91[ASN][1000 genomes]
rs62487619	0.93[ASN][1000 genomes]
rs6467776	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6467778	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6467780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6467782	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs6467783	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6944764	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6948094	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6954285	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs6959574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6963539	0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6970175	0.92[ASN][1000 genomes]
rs6974877	0.92[ASN][1000 genomes]
rs728092	0.84[ASN][1000 genomes]
rs749546	0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7795981	0.93[ASN][1000 genomes]
rs7808392	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs888609	0.89[ASN][1000 genomes]
rs9791462	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs9791634	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs985299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][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	esv34048	chr7:137724092-138213119	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831153	chr7:138078179-138265648	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1030956	chr7:138163169-138579519	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv981589	chr7:138163846-138177455	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1421604	S100A6	trans	parietal	SCAN
rs1421604	TRIM24	cis	parietal	SCAN
rs1421604	CHRM2	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:138147200-138183800	Weak transcription	Primary B cells from cord blood	blood
2	chr7:138147200-138189000	Weak transcription	Thymus	Thymus
3	chr7:138149800-138188600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:138153800-138184200	Weak transcription	Fetal Stomach	stomach
5	chr7:138155200-138184200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:138157600-138191400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr7:138160600-138182200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr7:138161800-138195800	Weak transcription	Fetal Brain Female	brain
9	chr7:138163600-138183400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr7:138163600-138184000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr7:138163600-138184200	Weak transcription	Aorta	Aorta
12	chr7:138163600-138184200	Weak transcription	Fetal Thymus	thymus
13	chr7:138164000-138191400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr7:138164000-138199800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:138164400-138176800	Weak transcription	Pancreas	Pancrea
16	chr7:138164400-138184200	Weak transcription	Ovary	ovary
17	chr7:138165000-138192000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr7:138165600-138184000	Weak transcription	Primary T cells from cord blood	blood
19	chr7:138166600-138184000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr7:138167000-138177800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr7:138168000-138181400	Weak transcription	Fetal Intestine Small	intestine
22	chr7:138168000-138196200	Weak transcription	Left Ventricle	heart
23	chr7:138168200-138178200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:138168800-138184200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr7:138169000-138190200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr7:138172800-138184400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr7:138173800-138183400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr7:138174600-138184200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr7:138174800-138177000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr7:138175200-138176600	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr7:138175200-138177000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr7:138175200-138201200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:138175400-138177400	Genic enhancers	HepG2	liver
34	chr7:138175400-138177600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr7:138175400-138185200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr7:138175600-138176800	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr7:138175800-138176600	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr7:138175800-138177600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr7:138175800-138183000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr7:138176000-138176600	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr7:138176000-138176600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr7:138176000-138176600	Enhancers	Stomach Mucosa	stomach
43	chr7:138176000-138176800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr7:138176000-138176800	Weak transcription	Lung	lung
45	chr7:138176000-138177600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr7:138176000-138180000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr7:138176000-138183400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr7:138176200-138176600	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr7:138176200-138178400	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr7:138176200-138180000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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