Variant report

Variant	rs7579078
Chromosome Location	chr2:231227439-231227440
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:231225373..231227509-chr2:231238018..231240508,2	MCF-7	breast:
2	chr2:231194037..231196548-chr2:231226140..231228040,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11891724	0.81[LWK][hapmap]
rs16827076	0.84[MEX][hapmap]
rs16827148	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs6712333	0.85[LWK][hapmap]
rs6742592	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6742630	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7563479	0.85[JPT][hapmap]
rs933961	0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv3417154	chr2:231159789-231258938	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3348338	chr2:231160124-231259498	Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv875945	chr2:231172642-231267925	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv869708	chr2:231173700-231267616	Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1004183	chr2:231174420-231258603	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv3486129	chr2:231175581-231265831	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv3486131	chr2:231175581-231265831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1013738	chr2:231176856-231258603	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv584667	chr2:231177822-231258450	Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv460119	chr2:231178876-231258450	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv584668	chr2:231178876-231258450	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv2751844	chr2:231179495-231280495	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv1001929	chr2:231179884-231258603	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv1006206	chr2:231179884-231268938	Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv584669	chr2:231183321-231258150	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv584670	chr2:231183786-231241276	ZNF genes & repeats Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv875946	chr2:231184106-231277567	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	esv3374323	chr2:231186424-231244177	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv875947	chr2:231190446-231281286	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7579078	CCL20	cis	parietal	SCAN
rs7579078	PSMD1	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231212800-231235600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:231212800-231236600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:231212800-231253600	Weak transcription	Gastric	stomach
4	chr2:231212800-231253600	Weak transcription	HMEC	breast
5	chr2:231212800-231259200	Weak transcription	Small Intestine	intestine
6	chr2:231212800-231262400	Weak transcription	K562	blood
7	chr2:231213000-231237600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:231220000-231275800	Weak transcription	Stomach Mucosa	stomach
9	chr2:231222200-231253400	Weak transcription	Colonic Mucosa	Colon
10	chr2:231222200-231273200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:231222400-231227600	Strong transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:231222400-231229800	Strong transcription	Liver	Liver
13	chr2:231222600-231228800	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr2:231222600-231228800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:231222600-231229200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:231222600-231233200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:231222800-231227600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:231222800-231231600	Weak transcription	Fetal Intestine Small	intestine
19	chr2:231223000-231227800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:231223200-231227800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:231223200-231237600	Weak transcription	Right Ventricle	heart
22	chr2:231223200-231253600	Weak transcription	NHLF	lung
23	chr2:231223400-231227800	Weak transcription	Psoas Muscle	Psoas
24	chr2:231223400-231229400	Strong transcription	Primary hematopoietic stem cells	blood
25	chr2:231223400-231235600	Weak transcription	NHDF-Ad	bronchial
26	chr2:231223400-231236200	Weak transcription	HUVEC	blood vessel
27	chr2:231223400-231237000	Weak transcription	NHEK	skin
28	chr2:231223400-231257800	Weak transcription	NH-A	brain
29	chr2:231223600-231263600	Weak transcription	Fetal Kidney	kidney
30	chr2:231223800-231228000	Strong transcription	Adipose Nuclei	Adipose
31	chr2:231223800-231228800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:231224200-231254000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:231224800-231228600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr2:231224800-231228800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:231225200-231268000	Weak transcription	Colon Smooth Muscle	Colon
36	chr2:231225400-231228800	Genic enhancers	Primary B cells from peripheral blood	blood
37	chr2:231225600-231228400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:231225600-231244600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:231226000-231228000	Genic enhancers	Primary T cells from cord blood	blood
40	chr2:231226000-231228000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:231226000-231228000	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr2:231226000-231228000	Strong transcription	Fetal Intestine Large	intestine
43	chr2:231226200-231227800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr2:231226200-231228200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
45	chr2:231226200-231231600	Weak transcription	Thymus	Thymus
46	chr2:231226400-231227600	Genic enhancers	Dnd41	blood
47	chr2:231226400-231227800	Genic enhancers	Primary T cells fromperipheralblood	blood
48	chr2:231226400-231227800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:231226400-231227800	Strong transcription	HepG2	liver
50	chr2:231226400-231228000	Genic enhancers	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links