Variant report

Variant	rs4651234
Chromosome Location	chr1:184799343-184799344
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	chr1:184796575..184799361-chr1:184927581..184929805,2	K562	blood:
2	chr1:184796346..184798314-chr1:184799191..184802086,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10797988	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10797989	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10797990	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1857954	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2135737	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs338562	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs338563	0.91[CHB][hapmap];0.89[CHD][hapmap]
rs338564	0.91[CHB][hapmap];0.89[CHD][hapmap]
rs338565	0.91[CHB][hapmap];0.89[CHD][hapmap]
rs338566	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs338567	0.91[CHB][hapmap];0.89[CHD][hapmap]
rs338568	0.91[CHB][hapmap];0.89[CHD][hapmap]
rs338570	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4011648	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4011650	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs520605	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs521366	0.87[EUR][1000 genomes]
rs533853	0.88[EUR][1000 genomes]
rs6424964	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6671637	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7519082	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs906285	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv917126	chr1:184655366-184902273	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv832048	chr1:184660146-184858802	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv508677	chr1:184778620-184825302	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv3843	chr1:184798670-184858114	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4651234	PRG4	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184768000-184809200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:184772400-184801800	Weak transcription	Primary T cells from cord blood	blood
3	chr1:184773200-184809400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:184783000-184807800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:184783200-184809200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:184783400-184803200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:184785400-184801200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:184786600-184805200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:184789800-184802000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:184790200-184809600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:184792200-184799400	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr1:184792200-184805200	Weak transcription	Fetal Intestine Small	intestine
13	chr1:184792800-184805200	Weak transcription	Small Intestine	intestine
14	chr1:184792800-184810000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr1:184793000-184805000	Weak transcription	K562	blood
16	chr1:184793000-184809600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr1:184793000-184813000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:184793400-184809200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:184793600-184799400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:184794400-184806200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:184795400-184802400	Weak transcription	Pancreas	Pancrea
22	chr1:184795400-184805800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:184795400-184822600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:184795800-184805400	Weak transcription	Adipose Nuclei	Adipose
25	chr1:184796800-184802000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:184797000-184806200	Weak transcription	Right Ventricle	heart
27	chr1:184797200-184805600	Weak transcription	NHLF	lung
28	chr1:184797200-184830000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:184797400-184799800	Enhancers	Fetal Heart	heart
30	chr1:184797600-184805000	Weak transcription	NHDF-Ad	bronchial
31	chr1:184797600-184807800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:184797800-184799400	Genic enhancers	Fetal Muscle Leg	muscle
33	chr1:184797800-184800600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:184797800-184800600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:184797800-184805200	Weak transcription	GM12878-XiMat	blood
36	chr1:184797800-184807400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:184797800-184807400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:184798000-184803000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:184798000-184807200	Weak transcription	NHEK	skin
40	chr1:184798200-184800600	Weak transcription	Left Ventricle	heart
41	chr1:184798400-184801200	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr1:184798400-184802800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:184798400-184805200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:184798400-184805200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:184798600-184801800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr1:184798800-184800600	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:184798800-184801000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:184799000-184799400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:184799000-184800000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:184799000-184801000	Strong transcription	Stomach Smooth Muscle	stomach

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