Variant report

Variant	rs3901486
Chromosome Location	chr4:166132731-166132732
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:166131315..166133290-chr4:166248025..166250572,2	MCF-7	breast:
2	chr4:166127800..166130090-chr4:166130347..166132969,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109466	Chromatin interaction
ENSG00000052802	Chromatin interaction
ENSG00000170088	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10517833	1.00[ASN][1000 genomes]
rs17488289	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17488436	1.00[ASN][1000 genomes]
rs17488814	0.89[ASN][1000 genomes]
rs17488835	0.89[ASN][1000 genomes]
rs17488877	0.89[ASN][1000 genomes]
rs17585396	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17585550	1.00[ASN][1000 genomes]
rs1818471	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1986031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35180362	0.90[EUR][1000 genomes]
rs36230153	0.89[ASN][1000 genomes]
rs3857013	0.81[EUR][1000 genomes]
rs4588420	1.00[ASN][1000 genomes]
rs55648903	1.00[ASN][1000 genomes]
rs55650232	1.00[ASN][1000 genomes]
rs55806488	0.90[ASN][1000 genomes]
rs56022310	1.00[ASN][1000 genomes]
rs56058696	1.00[ASN][1000 genomes]
rs56104713	1.00[ASN][1000 genomes]
rs56144732	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56287687	1.00[ASN][1000 genomes]
rs56326646	1.00[ASN][1000 genomes]
rs56370618	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56387271	0.89[ASN][1000 genomes]
rs56407727	1.00[ASN][1000 genomes]
rs56410965	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57162477	1.00[ASN][1000 genomes]
rs58426709	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6831119	1.00[ASN][1000 genomes]
rs6853219	1.00[ASN][1000 genomes]
rs72699595	1.00[ASN][1000 genomes]
rs72699598	1.00[ASN][1000 genomes]
rs72701606	1.00[ASN][1000 genomes]
rs72701608	1.00[ASN][1000 genomes]
rs72701655	0.89[ASN][1000 genomes]
rs72701660	0.89[ASN][1000 genomes]
rs72701663	0.89[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	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	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking 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 target site	29 gene(s)	inside rSNPs	diseases
4	nsv533191	chr4:165879671-166171638	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv881168	chr4:165975122-166196438	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv967809	chr4:166131906-166137884	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3901486	KLHL2	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166129600-166134600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:166129600-166137800	Weak transcription	Small Intestine	intestine
3	chr4:166129600-166154400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:166129600-166196800	Weak transcription	Pancreas	Pancrea
5	chr4:166129800-166133800	Weak transcription	Fetal Kidney	kidney
6	chr4:166129800-166142600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:166130200-166134600	Weak transcription	A549	lung
8	chr4:166130200-166135600	Weak transcription	Osteobl	bone
9	chr4:166130200-166137600	Weak transcription	HSMMtube	muscle
10	chr4:166130200-166150800	Weak transcription	Fetal Intestine Large	intestine
11	chr4:166130400-166133000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr4:166130400-166134000	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr4:166130400-166137200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:166130400-166138000	Weak transcription	Stomach Mucosa	stomach
15	chr4:166130400-166142400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:166130400-166143400	Weak transcription	Fetal Thymus	thymus
17	chr4:166130400-166143600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:166130400-166143600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:166130400-166143600	Weak transcription	HSMM	muscle
20	chr4:166130400-166176800	Weak transcription	Fetal Intestine Small	intestine
21	chr4:166130600-166133000	Enhancers	HMEC	breast
22	chr4:166130600-166133400	Enhancers	NHEK	skin
23	chr4:166130600-166134200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:166130600-166135600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr4:166130600-166136800	Weak transcription	Adipose Nuclei	Adipose
26	chr4:166130600-166137000	Weak transcription	NH-A	brain
27	chr4:166130600-166137800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr4:166130600-166142400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr4:166130600-166142400	Weak transcription	Right Ventricle	heart
30	chr4:166130600-166142800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr4:166130600-166143200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:166130600-166146200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:166130600-166200800	Weak transcription	Lung	lung
34	chr4:166130800-166133000	Active TSS	Brain Anterior Caudate	brain
35	chr4:166130800-166135400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr4:166130800-166135800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr4:166131200-166133000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr4:166131200-166142400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr4:166131200-166142600	Weak transcription	Psoas Muscle	Psoas
40	chr4:166131200-166143600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:166131400-166135400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr4:166131400-166148600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:166131600-166133800	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr4:166131600-166134400	Weak transcription	HUVEC	blood vessel
45	chr4:166131600-166135400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr4:166131600-166137800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:166131600-166138600	Weak transcription	Esophagus	oesophagus
48	chr4:166131600-166143200	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr4:166131600-166143400	Weak transcription	Dnd41	blood
50	chr4:166131600-166162800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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