Variant report

Variant	rs6665216
Chromosome Location	chr1:174893245-174893246
allele	A/G
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	chr1:174893134-174893486	H1-hESC	embryonic stem cell:	n/a	n/a
2	BATF	chr1:174892967-174893296	GM12878	blood:	n/a	chr1:174893144-174893155
3	NFIC	chr1:174892915-174893299	GM12878	blood:	n/a	n/a
4	EP300	chr1:174893043-174893245	GM12878	blood:	n/a	n/a
5	FOXM1	chr1:174892923-174893341	GM12878	blood:	n/a	n/a
6	BATF	chr1:174892966-174893298	GM12878	blood:	n/a	chr1:174893144-174893155

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174893186..174894907-chr1:174967344..174970326,2	K562	blood:

Variant related genes	Relation type
ENSG00000235869	TF binding region
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10436863	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1046439	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap]
rs11590474	1.00[LWK][hapmap]
rs12083837	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1653626	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap]
rs1653627	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs1653632	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs1754349	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1754351	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs1754355	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs1793297	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs1793300	0.80[EUR][1000 genomes]
rs1793309	0.86[EUR][1000 genomes]
rs1793319	0.82[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap]
rs1801791	0.86[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap]
rs1984418	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap]
rs2105949	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap]
rs2187562	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2285210	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap]
rs2981894	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2987869	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs2987874	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs3018410	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3118980	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap]
rs3133270	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs332795	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs332796	0.82[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap]
rs3753563	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.90[MKK][hapmap]
rs4233195	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs4650666	0.85[CEU][hapmap]
rs4651238	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55741955	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61828140	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61828142	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425305	1.00[ASW][hapmap];1.00[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];0.90[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6425309	0.81[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap]
rs6425310	0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap]
rs6656665	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6658861	0.82[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap]
rs6669560	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap]
rs66700013	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6688577	0.84[ASW][hapmap];0.85[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap]
rs7355181	0.84[TSI][hapmap]
rs7538588	1.00[ASW][hapmap];1.00[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];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7545910	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9700904	0.82[EUR][1000 genomes]
rs9804056	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs989423	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6665216	SLC9A11	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174861400-174902400	Weak transcription	Left Ventricle	heart
2	chr1:174872800-174900400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:174873400-174897200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:174874000-174910000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:174874200-174938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:174876800-174933600	Weak transcription	Aorta	Aorta
7	chr1:174883600-174900600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:174886000-174897000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:174886000-174907200	Weak transcription	Primary T cells from cord blood	blood
10	chr1:174886400-174896600	Weak transcription	Pancreas	Pancrea
11	chr1:174886400-174911600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:174888800-174897000	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:174889200-174897200	Weak transcription	Fetal Intestine Large	intestine
14	chr1:174889600-174897200	Weak transcription	Fetal Intestine Small	intestine
15	chr1:174889600-174907400	Weak transcription	Primary B cells from cord blood	blood
16	chr1:174889800-174896600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:174889800-174900000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:174890000-174899600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:174890000-174900600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:174891200-174893400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:174891600-174896600	Weak transcription	Gastric	stomach
22	chr1:174891800-174897000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:174891800-174908600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:174892200-174905000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:174892600-174899400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:174892600-174900000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:174893200-174893400	Enhancers	GM12878-XiMat	blood

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