Variant report

Variant	rs3890624
Chromosome Location	chr4:166251068-166251069
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:166126308..166130366-chr4:166247405..166251145,5	K562	blood:
2	chr4:166249129..166252121-chr4:166265324..166266921,2	K562	blood:

Variant related genes	Relation type
ENSG00000170088	Chromatin interaction
ENSG00000109466	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13353819	0.82[EUR][1000 genomes]
rs28678592	0.81[EUR][1000 genomes]
rs34317779	0.82[EUR][1000 genomes]
rs55672136	0.80[EUR][1000 genomes]
rs56058314	0.80[EUR][1000 genomes]
rs56245360	0.82[EUR][1000 genomes]
rs72701615	0.82[EUR][1000 genomes]
rs72701618	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv289926	chr4:166250805-166251867	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3890624	KLHL2	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166247000-166251600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:166247600-166251400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr4:166247600-166251600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr4:166247600-166251800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:166247800-166251200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr4:166247800-166251200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr4:166247800-166251400	Active TSS	H1 Cell Line	embryonic stem cell
8	chr4:166247800-166251400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:166247800-166251400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:166247800-166251400	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr4:166247800-166251400	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr4:166247800-166251400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:166247800-166251400	Active TSS	GM12878-XiMat	blood
14	chr4:166247800-166251400	Active TSS	NHDF-Ad	bronchial
15	chr4:166247800-166251600	Active TSS	Fetal Intestine Large	intestine
16	chr4:166247800-166251800	Active TSS	HSMMtube	muscle
17	chr4:166247800-166253600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:166248000-166251200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:166248000-166251200	Active TSS	Esophagus	oesophagus
20	chr4:166248000-166251200	Active TSS	HMEC	breast
21	chr4:166248000-166251400	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr4:166248000-166252000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:166248000-166253200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr4:166248000-166253600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:166249400-166251800	Flanking Active TSS	HUVEC	blood vessel
26	chr4:166249600-166251400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:166249600-166251600	Active TSS	Fetal Brain Male	brain
28	chr4:166249600-166254000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr4:166249600-166254000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr4:166249600-166266600	Weak transcription	Left Ventricle	heart
31	chr4:166249800-166251200	Enhancers	Primary B cells from peripheral blood	blood
32	chr4:166249800-166251600	Enhancers	Primary T cells from cord blood	blood
33	chr4:166249800-166251600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr4:166249800-166251800	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr4:166249800-166252200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr4:166249800-166255000	Weak transcription	Placenta	Placenta
37	chr4:166249800-166262400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr4:166249800-166262600	Weak transcription	Thymus	Thymus
39	chr4:166250000-166251400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr4:166250000-166251400	Active TSS	NH-A	brain
41	chr4:166250000-166252000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr4:166250000-166253600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr4:166250000-166254600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:166250000-166264600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr4:166250200-166251400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr4:166250200-166251400	Active TSS	Liver	Liver
47	chr4:166250200-166251600	Enhancers	Stomach Mucosa	stomach
48	chr4:166250200-166251800	Weak transcription	Gastric	stomach
49	chr4:166250200-166251800	Weak transcription	Lung	lung
50	chr4:166250200-166254000	Enhancers	Fetal Lung	lung

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