Variant report

Variant	rs9841810
Chromosome Location	chr3:196148055-196148056
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196133565..196136496-chr3:196147816..196149454,2	K562	blood:
2	chr3:196133998..196136496-chr3:196146393..196149316,3	K562	blood:
3	chr3:196146851..196150238-chr3:196157711..196160603,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225822	Chromatin interaction
ENSG00000163960	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10881567	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11185537	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12488531	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12638961	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13073879	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13089205	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28549737	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28594421	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35561509	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3973	0.82[JPT][hapmap]
rs4133244	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4290832	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4371545	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs4579046	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6583303	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6583305	0.82[JPT][hapmap]
rs6774540	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs6805994	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs73213970	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7373049	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7373103	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[MKK][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7373385	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7374841	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7617626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7624107	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7639524	1.00[JPT][hapmap]
rs9821735	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9839978	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9847223	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9848247	1.00[CEU][hapmap];0.88[CHD][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs9860931	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9874783	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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
15	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
16	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9841810	PCYT1A	Cis_1M	lymphoblastoid	RTeQTL
rs9841810	MGC33212	cis	multi-tissue	Pritchard

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196089600-196150000	Weak transcription	Small Intestine	intestine
2	chr3:196118600-196157400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:196125200-196157400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:196127000-196153800	Weak transcription	NHEK	skin
5	chr3:196127400-196152600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:196127600-196157400	Weak transcription	HUVEC	blood vessel
7	chr3:196128000-196149800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:196132200-196153800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:196132400-196150000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:196132600-196150000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:196132600-196157400	Weak transcription	Liver	Liver
12	chr3:196134000-196149800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:196134000-196150000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:196134000-196152600	Weak transcription	Fetal Intestine Large	intestine
15	chr3:196134000-196153800	Weak transcription	Primary B cells from cord blood	blood
16	chr3:196134000-196154400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:196134200-196149200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:196134200-196149600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:196134200-196149600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:196134200-196150000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:196134200-196153800	Weak transcription	Hela-S3	cervix
22	chr3:196134200-196154600	Weak transcription	Dnd41	blood
23	chr3:196134200-196157400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:196134400-196149400	Weak transcription	HSMM	muscle
25	chr3:196134400-196150400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr3:196134600-196157800	Weak transcription	A549	lung
27	chr3:196136000-196149800	Weak transcription	Fetal Lung	lung
28	chr3:196136200-196149600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:196136600-196150000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:196136600-196156800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:196136800-196149000	Weak transcription	Fetal Muscle Leg	muscle
32	chr3:196136800-196149800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:196137000-196149800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:196137000-196153000	Weak transcription	Thymus	Thymus
35	chr3:196137200-196149800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:196138200-196156600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:196138200-196157200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:196138400-196153000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:196139000-196150000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:196139400-196154000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:196141600-196149000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr3:196141600-196149000	Weak transcription	Pancreas	Pancrea
43	chr3:196141600-196149200	Weak transcription	Brain Angular Gyrus	brain
44	chr3:196141600-196157400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:196141600-196158000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr3:196142000-196149400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr3:196142000-196149600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:196142000-196149800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:196142000-196149800	Weak transcription	Osteobl	bone
50	chr3:196142000-196152000	Weak transcription	Primary T cells from cord blood	blood

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