Variant report

Variant	rs35541527
Chromosome Location	chr1:161734597-161734598
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	MXI1	chr1:161734401-161736955	SK-N-SH	brain:	n/a	n/a
2	GTF3C2	chr1:161734588-161735433	Hela-S3	cervix:	n/a	n/a
3	MYBL2	chr1:161734543-161735530	HepG2	liver:	n/a	n/a
4	ZNF384	chr1:161734536-161734832	GM12878	blood:	n/a	n/a
5	MAX	chr1:161734560-161735617	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:161718558..161723568-chr1:161731521..161737462,16	K562	blood:
2	chr1:161718568..161724937-chr1:161732191..161738837,13	K562	blood:
3	chr1:161718595..161726705-chr1:161728119..161739561,22	MCF-7	breast:

Variant related genes	Relation type
ATF6	TF binding region
ENSG00000081721	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10494361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs1063178	0.89[YRI][hapmap]
rs10917821	0.88[YRI][hapmap]
rs12121310	0.89[YRI][hapmap]
rs12121500	0.82[YRI][hapmap]
rs12745240	0.89[YRI][hapmap]
rs1394065	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16852851	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1891018	1.00[CHB][hapmap]
rs3767638	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4532807	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4996823	1.00[CHB][hapmap]
rs61104653	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73019349	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73019352	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74125007	0.95[EUR][1000 genomes]
rs74125022	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74125028	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs905593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs953301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.95[EUR][1000 genomes];0.84[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	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35541527	ATF6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161720400-161734600	Weak transcription	Aorta	Aorta
2	chr1:161720600-161734600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:161720600-161734800	Weak transcription	Psoas Muscle	Psoas
4	chr1:161720600-161736000	Weak transcription	Spleen	Spleen
5	chr1:161720800-161734600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:161720800-161735000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:161720800-161735000	Weak transcription	Stomach Mucosa	stomach
8	chr1:161721000-161734600	Weak transcription	Right Ventricle	heart
9	chr1:161721000-161734600	Weak transcription	HSMMtube	muscle
10	chr1:161721000-161735000	Weak transcription	Fetal Heart	heart
11	chr1:161721200-161734600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:161721200-161734800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:161723200-161734800	Weak transcription	Colonic Mucosa	Colon
14	chr1:161723400-161736000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:161724200-161735000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:161724600-161734600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:161724600-161734800	Weak transcription	Thymus	Thymus
18	chr1:161724600-161735000	Weak transcription	Fetal Brain Male	brain
19	chr1:161724600-161736000	Weak transcription	Small Intestine	intestine
20	chr1:161724800-161734600	Weak transcription	NHLF	lung
21	chr1:161724800-161736000	Weak transcription	Gastric	stomach
22	chr1:161725400-161735000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:161726000-161734600	Weak transcription	Fetal Kidney	kidney
24	chr1:161726000-161735800	Weak transcription	Esophagus	oesophagus
25	chr1:161726600-161734600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:161726800-161734600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:161726800-161734600	Weak transcription	NHEK	skin
28	chr1:161726800-161734800	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:161726800-161734800	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:161726800-161734800	Weak transcription	Fetal Lung	lung
31	chr1:161726800-161735000	Weak transcription	Primary T cells from cord blood	blood
32	chr1:161726800-161735000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:161726800-161735800	Weak transcription	Lung	lung
34	chr1:161727000-161734600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:161727000-161734600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr1:161727000-161735000	Weak transcription	Brain Substantia Nigra	brain
37	chr1:161727200-161734800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:161727200-161735000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:161727400-161735000	Weak transcription	Brain Angular Gyrus	brain
40	chr1:161727400-161735000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:161727800-161734600	Weak transcription	Ovary	ovary
42	chr1:161727800-161735000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:161728000-161734600	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr1:161728000-161734600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr1:161728000-161734600	Weak transcription	NHDF-Ad	bronchial
46	chr1:161728200-161734800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:161728400-161734600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr1:161728600-161734600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:161728600-161734600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:161728600-161734600	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links