Variant report

Variant	rs28495546
Chromosome Location	chr4:166209330-166209331
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:166208324..166210421-chr4:166212487..166214535,2	K562	blood:
2	chr4:166206637..166209635-chr4:166235769..166238670,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10005213	0.93[ASN][1000 genomes]
rs10009579	0.95[ASN][1000 genomes]
rs10010264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10015050	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10019675	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs10022944	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10031749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs10213218	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10213277	0.88[JPT][hapmap]
rs12108624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12171342	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12330937	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12331117	0.95[ASN][1000 genomes]
rs28397216	0.95[ASN][1000 genomes]
rs28520278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28525405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28621585	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28641126	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28669375	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28685193	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28853353	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[ASN][1000 genomes]
rs6834112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7665057	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9761388	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9991944	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs9992742	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9996084	0.89[ASN][1000 genomes]
rs9999376	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][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	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

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166144600-166218800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:166170000-166210000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:166170600-166209600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:166177200-166218800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:166177400-166215200	Weak transcription	Fetal Stomach	stomach
6	chr4:166177400-166216000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:166177400-166218600	Weak transcription	Spleen	Spleen
8	chr4:166177400-166219000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:166178800-166209400	Weak transcription	Brain Anterior Caudate	brain
10	chr4:166178800-166218800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:166178800-166218800	Weak transcription	Esophagus	oesophagus
12	chr4:166183800-166209600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr4:166183800-166215200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr4:166183800-166218800	Weak transcription	Aorta	Aorta
15	chr4:166192800-166223000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr4:166193200-166209400	Weak transcription	NHEK	skin
17	chr4:166195000-166210000	Weak transcription	Dnd41	blood
18	chr4:166195000-166215800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:166195600-166209400	Weak transcription	Adipose Nuclei	Adipose
20	chr4:166196200-166215800	Weak transcription	Left Ventricle	heart
21	chr4:166196200-166217600	Weak transcription	Gastric	stomach
22	chr4:166196600-166209800	Weak transcription	NH-A	brain
23	chr4:166197400-166210000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:166197600-166216000	Weak transcription	Pancreas	Pancrea
25	chr4:166198200-166230000	Weak transcription	Fetal Muscle Leg	muscle
26	chr4:166199600-166223000	Weak transcription	Ovary	ovary
27	chr4:166200200-166217200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr4:166200400-166210000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:166201000-166217200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:166201400-166209400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:166202400-166218800	Weak transcription	Brain Germinal Matrix	brain
32	chr4:166204200-166223000	Weak transcription	Thymus	Thymus
33	chr4:166204800-166221200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:166205600-166218800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:166205800-166209600	Weak transcription	Fetal Lung	lung
36	chr4:166206000-166218800	Weak transcription	Fetal Intestine Small	intestine
37	chr4:166206200-166215400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr4:166206200-166216600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:166206200-166218600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:166207000-166210400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr4:166207000-166210400	Enhancers	Primary B cells from peripheral blood	blood
42	chr4:166207000-166211000	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr4:166207800-166210400	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr4:166208000-166210200	Enhancers	Primary B cells from cord blood	blood
45	chr4:166208000-166217400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:166208600-166209600	Flanking Active TSS	GM12878-XiMat	blood
47	chr4:166208600-166210400	Enhancers	Liver	Liver
48	chr4:166208800-166209400	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr4:166208800-166210000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr4:166208800-166215200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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