Variant report

Variant	rs1801791
Chromosome Location	chr1:174961987-174961988
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	chr1:174959586-174962776	K562	blood:	n/a	n/a
2	POLR2A	chr1:174961977-174964877	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174737035..174739319-chr1:174960271..174963005,2	K562	blood:
2	chr1:174927580..174945830-chr1:174955726..174971213,32	K562	blood:

Variant related genes	Relation type
RNU6-307P	TF binding region
ENSG00000152061	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1046439	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590474	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs1754355	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs1978053	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1984418	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[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[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105949	1.00[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2187562	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs2187939	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285208	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285210	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2301507	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2987869	0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs2987874	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs3018410	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap]
rs3118980	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs3133270	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs3753563	0.86[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.84[AFR][1000 genomes]
rs4233195	0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs4651238	0.86[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.82[ASN][1000 genomes]
rs6425305	0.86[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap]
rs6425309	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425310	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6665216	0.86[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap]
rs6669560	1.00[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66700013	0.82[ASN][1000 genomes]
rs7514888	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7538588	0.86[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap]
rs9804056	0.86[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap]
rs989423	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]

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	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
2	nsv1001000	chr1:174944208-174978853	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1801791	SLC9A11	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174924200-174967800	Weak transcription	Brain Germinal Matrix	brain
2	chr1:174935000-174964000	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:174935000-174967000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:174937000-174963600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:174937400-174963600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:174938000-174963600	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr1:174938600-174965200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:174940000-174967600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:174940600-174962000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:174940600-174963600	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:174941000-174968000	Weak transcription	Gastric	stomach
12	chr1:174944400-174967800	Weak transcription	Aorta	Aorta
13	chr1:174944800-174967800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:174944800-174968000	Weak transcription	Spleen	Spleen
15	chr1:174946000-174968000	Weak transcription	Lung	lung
16	chr1:174949000-174967800	Weak transcription	Fetal Stomach	stomach
17	chr1:174950600-174964400	Weak transcription	NH-A	brain
18	chr1:174952200-174967800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:174952400-174968000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:174952800-174965800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:174954800-174968000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:174956000-174967800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:174956200-174967400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:174957200-174963200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:174959000-174965000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:174959600-174967400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:174960000-174965800	Weak transcription	HSMM	muscle
28	chr1:174960000-174967200	Weak transcription	Fetal Thymus	thymus
29	chr1:174960000-174967200	Weak transcription	Left Ventricle	heart
30	chr1:174960000-174967800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr1:174960000-174968000	Weak transcription	Esophagus	oesophagus
32	chr1:174960200-174963200	Weak transcription	Fetal Intestine Small	intestine
33	chr1:174960200-174963400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr1:174960200-174963400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:174960200-174963400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:174960200-174964000	Weak transcription	Fetal Kidney	kidney
37	chr1:174960200-174964200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:174960200-174964200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:174960200-174964200	Weak transcription	NHLF	lung
40	chr1:174960200-174964400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:174960200-174964400	Weak transcription	Osteobl	bone
42	chr1:174960200-174965000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:174960200-174965000	Weak transcription	K562	blood
44	chr1:174960200-174965200	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr1:174960200-174965800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr1:174960200-174966400	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:174960200-174967000	Weak transcription	Primary T cells from cord blood	blood
48	chr1:174960200-174967000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr1:174960200-174967000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr1:174960200-174967200	Weak transcription	Primary B cells from peripheral blood	blood

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