Variant report

Variant	rs3786544
Chromosome Location	chr19:55787869-55787870
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:55785041..55787227-chr19:55787483..55789658,2	K562	blood:
2	chr19:55781376..55784377-chr19:55785140..55788292,4	K562	blood:
3	chr19:55784752..55786541-chr19:55786945..55789658,2	K562	blood:
4	chr19:55786801..55789660-chr19:55815741..55818613,2	K562	blood:
5	chr19:55725155..55730672-chr19:55787708..55794060,8	K562	blood:
6	chr19:55769197..55771377-chr19:55786930..55788564,2	MCF-7	breast:
7	chr19:55727873..55730829-chr19:55787708..55791463,3	K562	blood:

Variant related genes	Relation type
ENSG00000267649	Chromatin interaction
ENSG00000105063	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10403164	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs10412187	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs10421676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11669468	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11672947	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4283339	0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.83[ASN][1000 genomes]
rs4806656	0.81[CEU][hapmap]
rs62126349	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7246293	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7257561	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912455	chr19:55725410-55879872	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
5	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
6	nsv912458	chr19:55763409-55823822	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55771400-55788400	Weak transcription	Stomach Mucosa	stomach
2	chr19:55771400-55790400	Weak transcription	HSMM	muscle
3	chr19:55771400-55790400	Weak transcription	NHDF-Ad	bronchial
4	chr19:55771400-55791600	Weak transcription	Fetal Heart	heart
5	chr19:55771600-55788000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr19:55771600-55790400	Weak transcription	HUVEC	blood vessel
7	chr19:55771800-55788000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:55772200-55790400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:55772400-55789800	Strong transcription	Fetal Muscle Trunk	muscle
10	chr19:55772800-55790200	Strong transcription	Fetal Stomach	stomach
11	chr19:55774400-55790400	Weak transcription	Psoas Muscle	Psoas
12	chr19:55777800-55788000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:55778000-55788200	Weak transcription	Brain Angular Gyrus	brain
14	chr19:55778200-55788200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr19:55778200-55790200	Weak transcription	Fetal Brain Male	brain
16	chr19:55778400-55790400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:55778400-55790400	Weak transcription	Fetal Kidney	kidney
18	chr19:55778600-55789200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr19:55778800-55789800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr19:55778800-55790200	Strong transcription	Fetal Intestine Small	intestine
21	chr19:55779000-55790200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:55779200-55789400	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr19:55779200-55789600	Strong transcription	Fetal Brain Female	brain
24	chr19:55779200-55789800	Strong transcription	Stomach Smooth Muscle	stomach
25	chr19:55779800-55788000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr19:55779800-55788800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr19:55780000-55790400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr19:55780000-55790400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr19:55780200-55789200	Strong transcription	Brain Germinal Matrix	brain
30	chr19:55780200-55789800	Strong transcription	Fetal Intestine Large	intestine
31	chr19:55780200-55789800	Strong transcription	Fetal Muscle Leg	muscle
32	chr19:55780400-55788400	Strong transcription	Spleen	Spleen
33	chr19:55780400-55789400	Strong transcription	Primary T cells from cord blood	blood
34	chr19:55780600-55789400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:55780600-55790200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:55780800-55789800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:55780800-55790600	Weak transcription	Small Intestine	intestine
38	chr19:55781000-55788000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr19:55781200-55789400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr19:55781200-55789800	Strong transcription	Dnd41	blood
41	chr19:55781200-55790200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr19:55781400-55788000	Weak transcription	NH-A	brain
43	chr19:55781400-55789200	Strong transcription	Liver	Liver
44	chr19:55781600-55788400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr19:55781600-55789600	Strong transcription	Lung	lung
46	chr19:55781800-55789400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr19:55782000-55789400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr19:55782400-55788600	Weak transcription	K562	blood
49	chr19:55782600-55789200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr19:55783000-55789200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links