Variant report

Variant	rs28612694
Chromosome Location	chr19:41086419-41086420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr19:41085886-41086429	K562	blood:	n/a	n/a
2	POLR2A	chr19:41086387-41086420	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41082477..41084504-chr19:41084701..41086992,2	K562	blood:
2	chr19:41073482..41079307-chr19:41080637..41087483,13	K562	blood:
3	chr19:41085326..41087014-chr19:41111763..41113290,2	K562	blood:
4	chr19:41083433..41086530-chr19:41091695..41093965,3	MCF-7	breast:
5	chr19:41084074..41087113-chr19:41095673..41098662,4	K562	blood:
6	chr19:41083100..41084650-chr19:41084700..41086878,2	MCF-7	breast:
7	chr19:41084714..41088277-chr19:41106890..41109795,3	K562	blood:

No data

Variant related genes	Relation type
SHKBP1	TF binding region
ENSG00000090006	Chromatin interaction
ENSG00000160460	Chromatin interaction
ENSG00000266164	Chromatin interaction
ENSG00000160410	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs10408716	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised 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	139 gene(s)	inside rSNPs	diseases
2	nsv911714	chr19:41006426-41165252	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv911715	chr19:41014922-41141434	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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	37 gene(s)	inside rSNPs	diseases
5	nsv911716	chr19:41023511-41109456	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv911717	chr19:41023511-41141434	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv911719	chr19:41033109-41147087	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv911720	chr19:41033109-41156940	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv911721	chr19:41040334-41124931	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	nsv869561	chr19:41077513-41139834	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41083600-41086600	Genic enhancers	Primary B cells from peripheral blood	blood
2	chr19:41083600-41091200	Weak transcription	Psoas Muscle	Psoas
3	chr19:41083600-41092800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:41083600-41093600	Weak transcription	Fetal Lung	lung
5	chr19:41083600-41095400	Weak transcription	Fetal Kidney	kidney
6	chr19:41083600-41100400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:41083600-41101000	Weak transcription	HSMMtube	muscle
8	chr19:41083800-41086800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:41083800-41086800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:41084000-41087800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr19:41084000-41089800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:41084000-41091600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr19:41084000-41094000	Weak transcription	HSMM	muscle
14	chr19:41084000-41095400	Strong transcription	Fetal Intestine Small	intestine
15	chr19:41084000-41097600	Strong transcription	Fetal Stomach	stomach
16	chr19:41084200-41086800	Weak transcription	Small Intestine	intestine
17	chr19:41084200-41089000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:41084200-41091200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr19:41084200-41093800	Weak transcription	NHEK	skin
20	chr19:41084200-41099800	Weak transcription	Fetal Brain Male	brain
21	chr19:41084400-41090800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr19:41084400-41091600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:41084400-41092000	Weak transcription	HepG2	liver
24	chr19:41084400-41094200	Weak transcription	HMEC	breast
25	chr19:41084400-41100000	Weak transcription	Stomach Mucosa	stomach
26	chr19:41084600-41091000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:41084600-41095200	Strong transcription	Fetal Muscle Leg	muscle
28	chr19:41084600-41097600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:41084600-41100400	Weak transcription	NHDF-Ad	bronchial
30	chr19:41084600-41102600	Weak transcription	Right Atrium	heart
31	chr19:41084800-41087000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr19:41084800-41089000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:41084800-41096600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr19:41084800-41097200	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr19:41084800-41097600	Strong transcription	Thymus	Thymus
36	chr19:41085000-41091000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr19:41085200-41086800	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
38	chr19:41085200-41087800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:41085200-41089200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr19:41085200-41089800	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr19:41085200-41090800	Strong transcription	Placenta	Placenta
42	chr19:41085200-41094000	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr19:41085400-41086600	Genic enhancers	GM12878-XiMat	blood
44	chr19:41085400-41086600	Strong transcription	HUVEC	blood vessel
45	chr19:41085400-41089600	Strong transcription	Esophagus	oesophagus
46	chr19:41085400-41089800	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr19:41085400-41090600	Strong transcription	Osteobl	bone
48	chr19:41085400-41094800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:41085400-41097200	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr19:41085600-41089800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links