Variant report

Variant	rs1435528
Chromosome Location	chr7:12249893-12249894
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	GATA3	chr7:12249761-12251069	T-47D	breast:	n/a	chr7:12250250-12250260 chr7:12250251-12250258 chr7:12250634-12250644 chr7:12250251-12250258 chr7:12250251-12250258 chr7:12250248-12250258
2	POLR2A	chr7:12249858-12251921	Hela-S3	cervix:	n/a	n/a
3	BRCA1	chr7:12249731-12251347	Hela-S3	cervix:	n/a	n/a
4	TBP	chr7:12249886-12251545	Hela-S3	cervix:	n/a	n/a
5	GATA2	chr7:12249808-12252102	SH-SY5Y	brain:	n/a	chr7:12251837-12251848 chr7:12250250-12250260 chr7:12251927-12251936 chr7:12250251-12250258 chr7:12250634-12250644 chr7:12251929-12251939 chr7:12250251-12250258 chr7:12250251-12250258 chr7:12251926-12251938 chr7:12250248-12250258
6	HCFC1	chr7:12249737-12252247	Hela-S3	cervix:	n/a	n/a
7	GATA3	chr7:12249708-12250935	SH-SY5Y	brain:	n/a	chr7:12250250-12250260 chr7:12250251-12250258 chr7:12250634-12250644 chr7:12250251-12250258 chr7:12250251-12250258 chr7:12250248-12250258
8	GATA2	chr7:12249853-12250964	HUVEC	blood vessel:	n/a	chr7:12250250-12250260 chr7:12250251-12250258 chr7:12250634-12250644 chr7:12250251-12250258 chr7:12250251-12250258 chr7:12250248-12250258
9	POLR2A	chr7:12249817-12252183	MCF10A-Er-Src	breast:	n/a	n/a
10	ZKSCAN1	chr7:12249837-12251913	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr7:12249858-12251684	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:12248340..12250610-chr7:12341759..12344659,2	K562	blood:
2	chr7:12245428..12248475-chr7:12248558..12250664,3	K562	blood:
3	chr7:12237815..12240381-chr7:12248250..12250812,3	K562	blood:

Variant related genes	Relation type
TMEM106B	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10260421	1.00[YRI][hapmap]
rs1042949	0.83[CHB][hapmap]
rs1060700	0.83[CHB][hapmap]
rs10950395	0.84[CHB][hapmap]
rs12667950	0.83[CHB][hapmap]
rs13230513	0.84[CHB][hapmap]
rs13309255	1.00[LWK][hapmap]
rs1435543	0.84[CHB][hapmap]
rs1468801	0.82[CHB][hapmap]
rs1468804	0.84[CHB][hapmap]
rs2043539	0.84[CHB][hapmap]
rs2160269	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs3173615	0.84[CHB][hapmap]
rs3800842	0.82[CHB][hapmap]
rs3800844	0.84[CHB][hapmap]
rs3800845	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs3823612	0.89[CHB][hapmap]
rs4721058	0.84[CHB][hapmap]
rs4721059	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs4721061	0.83[CHB][hapmap]
rs5011431	0.81[CHB][hapmap]
rs5011434	0.83[CHB][hapmap]
rs5011439	0.83[CHB][hapmap]
rs6460895	0.89[CHB][hapmap];0.81[CHD][hapmap]
rs6460898	0.84[CHB][hapmap]
rs6460900	0.89[CHB][hapmap];0.80[CHD][hapmap]
rs6460903	0.84[CHB][hapmap];0.81[CHD][hapmap]
rs6966915	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs7785087	0.84[CHB][hapmap]
rs7792410	0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv606199	chr7:11506143-12486659	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1021710	chr7:12164993-12251790	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1435528	PCBP2	trans	cerebellum	SCAN
rs1435528	ARL4A	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12249600-12250400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
2	chr7:12249600-12250400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr7:12249600-12250600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr7:12249800-12250000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr7:12249800-12250000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:12249800-12250000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
7	chr7:12249800-12250000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
8	chr7:12249800-12250000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
9	chr7:12249800-12250000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:12249800-12250000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:12249800-12250000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
12	chr7:12249800-12250000	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr7:12249800-12250000	Bivalent/Poised TSS	Primary B cells from cord blood	blood
14	chr7:12249800-12250000	Enhancers	Primary T cells from cord blood	blood
15	chr7:12249800-12250000	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr7:12249800-12250000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr7:12249800-12250000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr7:12249800-12250000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
19	chr7:12249800-12250000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr7:12249800-12250000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr7:12249800-12250000	Flanking Active TSS	Liver	Liver
22	chr7:12249800-12250000	Flanking Active TSS	Colon Smooth Muscle	Colon
23	chr7:12249800-12250000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr7:12249800-12250000	Enhancers	Fetal Heart	heart
25	chr7:12249800-12250000	Flanking Active TSS	Fetal Intestine Large	intestine
26	chr7:12249800-12250000	Flanking Active TSS	Fetal Lung	lung
27	chr7:12249800-12250000	Enhancers	Fetal Stomach	stomach
28	chr7:12249800-12250000	Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr7:12249800-12250000	Enhancers	Stomach Mucosa	stomach
30	chr7:12249800-12250000	Flanking Active TSS	A549	lung
31	chr7:12249800-12250000	Flanking Active TSS	Hela-S3	cervix
32	chr7:12249800-12250000	Active TSS	HMEC	breast
33	chr7:12249800-12250000	Flanking Active TSS	NHDF-Ad	bronchial
34	chr7:12249800-12250000	Flanking Active TSS	NHEK	skin
35	chr7:12249800-12250000	Active TSS	Osteobl	bone
36	chr7:12249800-12250200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
37	chr7:12249800-12250200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
38	chr7:12249800-12250200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr7:12249800-12250200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr7:12249800-12250200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr7:12249800-12250200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr7:12249800-12250200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr7:12249800-12250200	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr7:12249800-12250200	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr7:12249800-12250200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
46	chr7:12249800-12250200	Flanking Active TSS	Rectal Smooth Muscle	rectum
47	chr7:12249800-12250200	Flanking Active TSS	HepG2	liver
48	chr7:12249800-12250200	Flanking Active TSS	HUVEC	blood vessel
49	chr7:12249800-12250200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
50	chr7:12249800-12250400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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