Variant report

Variant	rs7625886
Chromosome Location	chr3:195952900-195952901
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:195952367..195954245-chr3:195957237..195960071,2	K562	blood:
2	chr3:195951103..195953764-chr3:195954363..195955891,2	K562	blood:
3	chr3:195952863..195955052-chr3:195973498..195975966,2	K562	blood:

Variant related genes	Relation type
ENSG00000161217	Chromatin interaction
ENSG00000163959	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12491227	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs12630070	0.83[JPT][hapmap]
rs12637288	0.85[JPT][hapmap]
rs1476331	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs1476332	0.92[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs1948690	0.91[JPT][hapmap]
rs2047551	0.85[JPT][hapmap]
rs2088666	0.85[JPT][hapmap]
rs3772109	0.85[JPT][hapmap]
rs4916421	0.85[JPT][hapmap]
rs4916440	0.94[ASN][1000 genomes]
rs4916441	0.89[ASN][1000 genomes]
rs58021463	0.94[ASN][1000 genomes]
rs68119320	0.94[ASN][1000 genomes]
rs712012	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7636149	0.85[JPT][hapmap]
rs7639752	0.83[JPT][hapmap]
rs870339	0.85[JPT][hapmap]
rs9343	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs939883	0.87[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	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
5	nsv878171	chr3:195677895-195959924	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv1008512	chr3:195709662-195974936	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
8	nsv1009105	chr3:195769609-195984388	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
10	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
11	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
12	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
13	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
14	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
15	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
16	nsv878175	chr3:195907653-195973244	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
17	nsv1014159	chr3:195908999-195968512	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
18	nsv878176	chr3:195926234-195959924	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv878178	chr3:195929268-195998451	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
20	nsv878179	chr3:195929268-196019680	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
21	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
22	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS 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	33 gene(s)	inside rSNPs	diseases
23	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
24	nsv521280	chr3:195949541-195955472	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised 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
rs7625886	PCYT1A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195944200-195964000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:195945000-195968400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:195946600-195954200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:195946600-195955000	Weak transcription	Right Atrium	heart
5	chr3:195946600-195965600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:195946800-195954200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:195946800-195962600	Weak transcription	Primary T cells from cord blood	blood
8	chr3:195946800-195964200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:195946800-195967400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:195947000-195954200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:195947000-195954200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:195947000-195954400	Weak transcription	Fetal Brain Female	brain
13	chr3:195947000-195954600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:195947000-195959000	Weak transcription	Dnd41	blood
15	chr3:195947000-195960800	Weak transcription	Fetal Intestine Large	intestine
16	chr3:195947000-195963800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:195947000-195964000	Weak transcription	Colonic Mucosa	Colon
18	chr3:195947200-195954000	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:195947200-195962000	Weak transcription	Fetal Brain Male	brain
20	chr3:195947200-195962600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:195947200-195962600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:195947400-195958800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:195948000-195970400	Strong transcription	Liver	Liver
24	chr3:195949000-195953800	Weak transcription	Fetal Intestine Small	intestine
25	chr3:195950400-195953800	Weak transcription	Placenta	Placenta
26	chr3:195950400-195959800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:195950400-195964400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:195950600-195954000	Weak transcription	HSMMtube	muscle
29	chr3:195950600-195954200	Weak transcription	Pancreas	Pancrea
30	chr3:195950600-195954400	Weak transcription	HSMM	muscle
31	chr3:195951400-195954000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr3:195951800-195955800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr3:195952200-195954600	Enhancers	HepG2	liver
34	chr3:195952400-195953800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:195952600-195963200	Weak transcription	K562	blood

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