Variant report

Variant	rs7258854
Chromosome Location	chr19:43027819-43027820
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:43015384..43018230-chr19:43027270..43028930,2	MCF-7	breast:
2	chr19:43023426..43026592-chr19:43026629..43028829,3	K562	blood:
3	chr19:43026349..43028606-chr19:43031972..43033644,2	K562	blood:
4	chr19:43027445..43029182-chr19:43031157..43032882,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079385	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10401178	1.00[CEU][hapmap]
rs10404589	1.00[CEU][hapmap]
rs10405152	1.00[CEU][hapmap]
rs10405410	1.00[CEU][hapmap]
rs10406800	1.00[TSI][hapmap]
rs10407155	1.00[TSI][hapmap]
rs10411498	1.00[TSI][hapmap]
rs10416108	1.00[CEU][hapmap]
rs10416535	1.00[TSI][hapmap]
rs10421409	1.00[TSI][hapmap]
rs10423959	1.00[TSI][hapmap]
rs10423978	1.00[TSI][hapmap]
rs10424206	1.00[CEU][hapmap]
rs11878991	1.00[CEU][hapmap]
rs11880554	1.00[CEU][hapmap]
rs11881583	1.00[CEU][hapmap]
rs11883406	1.00[CEU][hapmap]
rs11883425	1.00[CEU][hapmap]
rs13343322	1.00[TSI][hapmap]
rs16975799	1.00[CEU][hapmap]
rs2229614	1.00[TSI][hapmap]
rs6509015	1.00[CEU][hapmap]
rs6509019	1.00[CEU][hapmap]
rs7246161	1.00[CEU][hapmap]
rs7246232	1.00[TSI][hapmap]
rs7246591	1.00[CEU][hapmap]
rs7247278	1.00[CEU][hapmap]
rs7248473	1.00[TSI][hapmap]
rs8099885	1.00[TSI][hapmap]
rs8105525	1.00[CEU][hapmap]
rs8109258	1.00[TSI][hapmap]

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	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
3	esv2422468	chr19:42991289-43669027	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1057390	chr19:43003323-43173028	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:43003200-43030600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr19:43003400-43028400	Weak transcription	Esophagus	oesophagus
3	chr19:43003400-43029400	Weak transcription	Small Intestine	intestine
4	chr19:43006200-43029800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr19:43012200-43028200	Strong transcription	Liver	Liver
6	chr19:43013800-43032000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr19:43015600-43030800	Weak transcription	Left Ventricle	heart
8	chr19:43016000-43032400	Weak transcription	Brain Anterior Caudate	brain
9	chr19:43016600-43029400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr19:43016600-43031800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:43017400-43031400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr19:43018200-43030400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr19:43019000-43029200	Weak transcription	Stomach Mucosa	stomach
14	chr19:43020400-43030400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:43022000-43028200	Strong transcription	Duodenum Mucosa	Duodenum
16	chr19:43022000-43028400	Genic enhancers	HepG2	liver
17	chr19:43022200-43028600	Strong transcription	Fetal Intestine Small	intestine
18	chr19:43023200-43032400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr19:43023600-43029600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr19:43023600-43031600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:43023600-43032200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:43023600-43033200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr19:43025000-43030400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr19:43025400-43028200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr19:43025600-43032000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr19:43025600-43032400	Weak transcription	Right Ventricle	heart
27	chr19:43026000-43028000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr19:43026000-43028000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:43026000-43029000	Weak transcription	Gastric	stomach
30	chr19:43026000-43030400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr19:43026200-43028200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr19:43026200-43028400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr19:43026200-43028400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr19:43026200-43028600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr19:43026200-43032800	Weak transcription	Fetal Stomach	stomach
36	chr19:43026400-43029800	Weak transcription	Primary T cells from cord blood	blood
37	chr19:43026800-43028400	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr19:43027200-43028800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr19:43027200-43029200	Enhancers	Primary hematopoietic stem cells	blood
40	chr19:43027400-43028400	Weak transcription	Adipose Nuclei	Adipose
41	chr19:43027400-43028400	Weak transcription	Spleen	Spleen
42	chr19:43027400-43029000	Weak transcription	Fetal Intestine Large	intestine
43	chr19:43027400-43030000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr19:43027600-43028000	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr19:43027600-43028000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr19:43027600-43028200	Weak transcription	Colonic Mucosa	Colon
47	chr19:43027600-43028600	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr19:43027600-43028800	Enhancers	GM12878-XiMat	blood
49	chr19:43027600-43029200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:43027600-43030400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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