Variant report

Variant	rs10849133
Chromosome Location	chr12:4830000-4830001
allele	G/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	HDAC2	chr12:4829691-4830226	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP1	chr12:4829769-4830279	H1-hESC	embryonic stem cell:	n/a	n/a
3	HDAC2	chr12:4829838-4830127	H1-hESC	embryonic stem cell:	n/a	n/a
4	BACH1	chr12:4829810-4830234	H1-hESC	embryonic stem cell:	n/a	n/a
5	GTF2F1	chr12:4829917-4830083	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTBP2	chr12:4829623-4830143	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr12:4829900-4830389	H1-hESC	embryonic stem cell:	n/a	n/a
8	TBP	chr12:4829815-4830164	H1-hESC	embryonic stem cell:	n/a	n/a
9	ATF2	chr12:4829583-4830213	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr12:4829942-4830216	H1-hESC	embryonic stem cell:	n/a	n/a
11	ATF2	chr12:4829776-4830202	H1-hESC	embryonic stem cell:	n/a	n/a
12	TEAD4	chr12:4829777-4830160	H1-hESC	embryonic stem cell:	n/a	n/a
13	CHD2	chr12:4829781-4830183	H1-hESC	embryonic stem cell:	n/a	n/a
14	TCF12	chr12:4829939-4830124	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000255474	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10047570	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10083146	0.81[ASN][1000 genomes]
rs1009633	0.86[CHB][hapmap]
rs10160902	0.89[ASN][1000 genomes]
rs1024655	0.82[ASN][1000 genomes]
rs10431361	0.90[ASN][1000 genomes]
rs10431362	0.88[ASN][1000 genomes]
rs10774256	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs10774267	0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10849125	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10849126	0.84[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10849127	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10849128	0.88[ASN][1000 genomes]
rs10849129	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10849130	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10849131	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10849137	0.95[ASN][1000 genomes]
rs10849138	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10849139	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10849143	0.89[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs11063314	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11063318	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11063327	0.94[ASN][1000 genomes]
rs11063328	0.92[ASN][1000 genomes]
rs11063331	0.91[ASN][1000 genomes]
rs12296205	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12320374	0.95[ASN][1000 genomes]
rs1468556	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs17783373	0.89[ASN][1000 genomes]
rs1990310	0.81[ASN][1000 genomes]
rs2109099	0.89[ASN][1000 genomes]
rs2109100	0.89[ASN][1000 genomes]
rs2159354	0.90[ASN][1000 genomes]
rs2159355	0.90[ASN][1000 genomes]
rs2191157	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs2240762	0.85[CHB][hapmap]
rs2267552	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs2286578	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286580	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs2286581	0.86[CHB][hapmap];0.93[CHD][hapmap];0.84[ASN][1000 genomes]
rs2286582	0.86[CHB][hapmap];0.93[CHD][hapmap];0.84[ASN][1000 genomes]
rs2359466	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2359467	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.95[ASN][1000 genomes]
rs35049745	0.89[ASN][1000 genomes]
rs3782740	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3782741	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3782742	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.96[ASN][1000 genomes]
rs4147696	0.81[ASN][1000 genomes]
rs4765779	0.89[ASN][1000 genomes]
rs4765780	0.86[ASN][1000 genomes]
rs4765781	0.88[ASN][1000 genomes]
rs4765782	0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs4766272	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4766276	0.89[ASN][1000 genomes]
rs4766278	0.89[ASN][1000 genomes]
rs4766279	0.89[ASN][1000 genomes]
rs4766280	0.89[ASN][1000 genomes]
rs4766281	0.89[ASN][1000 genomes]
rs4766282	1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs4766283	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs4766286	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6489558	0.95[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs6489560	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[ASN][1000 genomes]
rs6489565	0.95[ASN][1000 genomes]
rs6489566	0.95[ASN][1000 genomes]
rs6489567	0.94[ASN][1000 genomes]
rs7132030	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7136583	0.83[ASN][1000 genomes]
rs7137040	0.89[ASN][1000 genomes]
rs7137660	0.89[ASN][1000 genomes]
rs7295230	0.94[ASN][1000 genomes]
rs7295251	0.94[ASN][1000 genomes]
rs7297290	0.84[ASN][1000 genomes]
rs7305387	0.95[ASN][1000 genomes]
rs7305525	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs7306235	0.89[ASN][1000 genomes]
rs7311475	0.89[ASN][1000 genomes]
rs7311675	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7311694	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7312119	0.89[ASN][1000 genomes]
rs7314849	0.94[ASN][1000 genomes]
rs7315211	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7316209	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7953170	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7953399	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7953482	0.94[ASN][1000 genomes]
rs7966628	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7967117	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7970126	0.89[ASN][1000 genomes]
rs7972019	0.89[ASN][1000 genomes]
rs7972501	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs7975978	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7976011	0.95[ASN][1000 genomes]
rs7976219	0.84[ASN][1000 genomes]
rs929481	0.91[ASN][1000 genomes]
rs9300304	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.80[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	nsv832318	chr12:4655799-4875837	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1054218	chr12:4819576-4882667	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10849133	WNK1	cis	parietal	SCAN
rs10849133	SLC2A14	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4811200-4833600	Weak transcription	Brain Germinal Matrix	brain
2	chr12:4825800-4838200	Weak transcription	Gastric	stomach
3	chr12:4826800-4830400	Enhancers	H1 Cell Line	embryonic stem cell
4	chr12:4827200-4830400	Enhancers	H9 Cell Line	embryonic stem cell
5	chr12:4827400-4849600	Weak transcription	Fetal Brain Female	brain
6	chr12:4828200-4830600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:4828400-4830400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr12:4828600-4830400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:4828600-4830400	Active TSS	Rectal Smooth Muscle	rectum
10	chr12:4828600-4830600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:4828800-4830000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:4829000-4830000	Active TSS	Colonic Mucosa	Colon
13	chr12:4829000-4830600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:4829000-4830600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr12:4829200-4830000	Flanking Active TSS	Fetal Intestine Large	intestine
16	chr12:4829200-4830600	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr12:4829200-4831400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:4829600-4830200	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr12:4829600-4830400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr12:4829600-4830400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr12:4829600-4830400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr12:4829600-4830400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr12:4829600-4830400	Flanking Active TSS	Fetal Intestine Small	intestine
24	chr12:4829600-4830400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr12:4829600-4830600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr12:4829800-4830000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:4829800-4830000	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr12:4830000-4830200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:4830000-4830200	Enhancers	Colonic Mucosa	Colon
30	chr12:4830000-4830400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr12:4830000-4830400	Bivalent Enhancer	Placenta	Placenta
32	chr12:4830000-4830400	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr12:4830000-4830600	Enhancers	Fetal Intestine Large	intestine

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