Variant report

Variant	rs7619976
Chromosome Location	chr3:155591198-155591199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:155461486..155465793-chr3:155586998..155592801,6	K562	blood:
2	chr3:155461523..155464397-chr3:155587900..155591398,5	MCF-7	breast:
3	chr3:155568718..155574348-chr3:155586235..155593210,15	K562	blood:
4	chr3:155546434..155549740-chr3:155588922..155591609,3	K562	blood:
5	chr3:155522036..155526613-chr3:155586597..155592084,8	K562	blood:
6	chr3:155508129..155511910-chr3:155589025..155592150,5	K562	blood:
7	chr3:155587045..155589767-chr3:155590571..155592335,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163655	Chromatin interaction
ENSG00000114805	Chromatin interaction
ENSG00000174928	Chromatin interaction
ENSG00000214919	Chromatin interaction
ENSG00000169359	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10804773	0.99[ASN][1000 genomes]
rs10804774	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936020	0.97[ASN][1000 genomes]
rs1131925	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11714133	0.95[ASN][1000 genomes]
rs13059611	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13091683	0.86[ASN][1000 genomes]
rs2054878	0.85[ASN][1000 genomes]
rs2063903	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34337666	0.89[ASN][1000 genomes]
rs35321137	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35472369	0.85[ASN][1000 genomes]
rs3772115	0.93[ASN][1000 genomes]
rs3772116	0.94[ASN][1000 genomes]
rs3821365	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680219	0.97[ASN][1000 genomes]
rs4680223	0.90[ASN][1000 genomes]
rs6441028	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66509404	0.99[ASN][1000 genomes]
rs6763830	0.82[ASN][1000 genomes]
rs6799267	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7633168	0.98[ASN][1000 genomes]
rs7643630	0.89[ASN][1000 genomes]
rs7651038	0.91[ASN][1000 genomes]
rs7652005	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2753744	chr3:155487298-155707298	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats 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 miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv877681	chr3:155535670-155654017	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7619976	SLC33A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155588000-155591800	Active TSS	K562	blood
2	chr3:155589600-155599600	Weak transcription	Spleen	Spleen
3	chr3:155589800-155592800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:155589800-155596600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:155589800-155596600	Weak transcription	Lung	lung
6	chr3:155589800-155607000	Weak transcription	Pancreas	Pancrea
7	chr3:155590000-155591400	Enhancers	Primary B cells from peripheral blood	blood
8	chr3:155590000-155592800	Weak transcription	Aorta	Aorta
9	chr3:155590000-155592800	Weak transcription	Psoas Muscle	Psoas
10	chr3:155590000-155593000	Weak transcription	Gastric	stomach
11	chr3:155590000-155599400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:155590200-155591200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:155590200-155591200	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr3:155590200-155591200	Enhancers	Fetal Intestine Small	intestine
15	chr3:155590200-155591400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr3:155590200-155591400	Enhancers	Fetal Thymus	thymus
17	chr3:155590200-155591600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr3:155590200-155592600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:155590200-155592800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:155590200-155592800	Weak transcription	Ovary	ovary
21	chr3:155590200-155593000	Weak transcription	Left Ventricle	heart
22	chr3:155590200-155593000	Weak transcription	Right Atrium	heart
23	chr3:155590200-155594000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:155590200-155596600	Weak transcription	Thymus	Thymus
25	chr3:155590200-155599000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:155590200-155599400	Weak transcription	Right Ventricle	heart
27	chr3:155590200-155608400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:155590200-155643000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:155590200-155667400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:155590400-155591200	Enhancers	Primary hematopoietic stem cells	blood
31	chr3:155590400-155591200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr3:155590400-155591400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:155590400-155591400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:155590400-155591400	Enhancers	Fetal Lung	lung
35	chr3:155590400-155591400	Enhancers	NHEK	skin
36	chr3:155590400-155591800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:155590400-155591800	Weak transcription	NHDF-Ad	bronchial
38	chr3:155590400-155592800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:155590400-155592800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:155590400-155593200	Weak transcription	Fetal Heart	heart
41	chr3:155590400-155593800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:155590400-155594200	Weak transcription	Fetal Stomach	stomach
43	chr3:155590400-155594800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:155590400-155596600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:155590600-155591200	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:155590600-155592000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:155590600-155593000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:155590600-155597800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:155590800-155591200	Enhancers	HepG2	liver
50	chr3:155590800-155591400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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