Variant report

Variant	rs28549737
Chromosome Location	chr3:196140367-196140368
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196136760..196139527-chr3:196139977..196142790,2	K562	blood:
2	chr3:196044447..196045990-chr3:196139208..196141957,2	MCF-7	breast:
3	chr3:196138176..196140569-chr3:196226942..196228528,2	MCF-7	breast:
4	chr3:196136134..196138094-chr3:196139731..196142693,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235897	Chromatin interaction
ENSG00000272741	Chromatin interaction
ENSG00000213123	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10881567	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11185537	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12488531	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12638961	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13073879	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13089205	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28594421	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35561509	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4133244	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4290832	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4579046	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6583303	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73213970	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7373049	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7373103	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7373385	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7374841	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7624107	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9821735	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9839978	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9841810	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9847223	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9874783	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
4	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
7	nsv1003764	chr3:196028141-196190687	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv536895	chr3:196028141-196190687	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	esv1844755	chr3:196057616-196190350	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv469831	chr3:196071603-196235225	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	nsv482542	chr3:196071603-196235225	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv878183	chr3:196072442-196181228	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
14	esv32642	chr3:196118819-196153861	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28549737	PCYT1A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196083600-196143800	Weak transcription	Psoas Muscle	Psoas
2	chr3:196089600-196150000	Weak transcription	Small Intestine	intestine
3	chr3:196095600-196144400	Weak transcription	Fetal Heart	heart
4	chr3:196118600-196157400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:196124600-196147400	Weak transcription	Right Atrium	heart
6	chr3:196125200-196157400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:196127000-196141200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:196127000-196141400	Weak transcription	HMEC	breast
9	chr3:196127000-196153800	Weak transcription	NHEK	skin
10	chr3:196127400-196141200	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:196127400-196152600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:196127600-196142800	Weak transcription	Spleen	Spleen
13	chr3:196127600-196145000	Weak transcription	Right Ventricle	heart
14	chr3:196127600-196147600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:196127600-196157400	Weak transcription	HUVEC	blood vessel
16	chr3:196127800-196141200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:196127800-196141200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:196127800-196141600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr3:196128000-196149800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:196129800-196144800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:196132200-196145800	Weak transcription	Lung	lung
22	chr3:196132200-196153800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:196132400-196150000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:196132600-196150000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:196132600-196157400	Weak transcription	Liver	Liver
26	chr3:196134000-196141200	Weak transcription	Pancreas	Pancrea
27	chr3:196134000-196143000	Weak transcription	Ovary	ovary
28	chr3:196134000-196144200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:196134000-196144400	Weak transcription	Fetal Stomach	stomach
30	chr3:196134000-196147800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:196134000-196149800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:196134000-196150000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:196134000-196152600	Weak transcription	Fetal Intestine Large	intestine
34	chr3:196134000-196153800	Weak transcription	Primary B cells from cord blood	blood
35	chr3:196134000-196154400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:196134200-196141200	Weak transcription	HepG2	liver
37	chr3:196134200-196145400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:196134200-196146400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:196134200-196146400	Weak transcription	Brain Anterior Caudate	brain
40	chr3:196134200-196146400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr3:196134200-196147600	Weak transcription	K562	blood
42	chr3:196134200-196149200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:196134200-196149600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:196134200-196149600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:196134200-196150000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:196134200-196153800	Weak transcription	Hela-S3	cervix
47	chr3:196134200-196154600	Weak transcription	Dnd41	blood
48	chr3:196134200-196157400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr3:196134400-196141400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:196134400-196149400	Weak transcription	HSMM	muscle

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