Variant report

Variant	rs61615159
Chromosome Location	chr3:196048593-196048594
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196043702..196046805-chr3:196047566..196053193,12	MCF-7	breast:
2	chr3:196047230..196049663-chr3:196050075..196051635,2	MCF-7	breast:
3	chr3:196045968..196048750-chr3:196049262..196052287,4	K562	blood:
4	chr3:196045621..196048927-chr3:196067958..196070489,3	MCF-7	breast:
5	chr3:196047776..196049836-chr3:196051866..196054572,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213123	Chromatin interaction
ENSG00000145107	Chromatin interaction
ENSG00000235897	Chromatin interaction
ENSG00000272741	Chromatin interaction
ENSG00000212146	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12487600	0.82[AFR][1000 genomes]
rs12497601	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2047549	0.81[EUR][1000 genomes]
rs2280526	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56346343	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56393817	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56845593	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60670584	0.81[AFR][1000 genomes]
rs61134797	0.83[AFR][1000 genomes]
rs6777819	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6782336	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67844518	0.81[AFR][1000 genomes]
rs6785339	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73212183	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	nsv4183	chr3:196034067-196079109	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs61615159	TM4SF19	cis	Muscle Skeletal	GTEx
rs61615159	SLC51A	cis	Heart Left Ventricle	GTEx
rs61615159	PCYT1A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196045600-196048600	Weak transcription	Thymus	Thymus
2	chr3:196045600-196053800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:196045600-196054000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:196045600-196054000	Weak transcription	Pancreas	Pancrea
5	chr3:196045600-196054200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:196045600-196054200	Weak transcription	Ovary	ovary
7	chr3:196045800-196052400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:196045800-196052800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:196045800-196053000	Weak transcription	Fetal Intestine Small	intestine
10	chr3:196045800-196054200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:196046000-196050200	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:196046000-196050800	Weak transcription	HSMM	muscle
13	chr3:196046000-196053600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:196046000-196054400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:196046200-196050600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr3:196046200-196051000	Weak transcription	Brain Substantia Nigra	brain
17	chr3:196046200-196054200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:196046400-196048800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr3:196046600-196050200	Weak transcription	Hela-S3	cervix
20	chr3:196047200-196050000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr3:196047200-196054600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:196047400-196050000	Weak transcription	K562	blood
23	chr3:196047400-196053800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:196047400-196054200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:196047600-196048800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:196047600-196050600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr3:196047600-196050800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:196047600-196053800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:196047600-196053800	Weak transcription	HMEC	breast
30	chr3:196047600-196054400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:196047600-196063600	Weak transcription	NHEK	skin
32	chr3:196047800-196048600	Weak transcription	HepG2	liver
33	chr3:196048000-196049200	Enhancers	Fetal Thymus	thymus
34	chr3:196048400-196048800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:196048400-196050000	Enhancers	Monocytes-CD14+_RO01746	blood

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