Variant report

Variant	rs6799267
Chromosome Location	chr3:155601734-155601735
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:155587045..155592306-chr3:155600737..155605779,6	MCF-7	breast:
2	chr3:155593242..155596780-chr3:155599483..155602658,3	MCF-7	breast:
3	chr3:155588362..155590227-chr3:155599878..155601877,2	MCF-7	breast:
4	chr3:155601296..155605428-chr3:155605959..155609229,4	MCF-7	breast:
5	chr3:155601596..155603326-chr3:155623926..155626265,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163655	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10804773	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10804774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10936020	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1131925	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11714133	0.92[ASN][1000 genomes]
rs13059611	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13091683	0.83[ASN][1000 genomes]
rs2054878	0.81[ASN][1000 genomes]
rs2063903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2200707	0.85[JPT][hapmap]
rs34337666	0.86[ASN][1000 genomes]
rs35321137	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35472369	0.81[ASN][1000 genomes]
rs3772115	0.90[ASN][1000 genomes]
rs3772116	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3821365	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680219	0.93[ASN][1000 genomes]
rs4680223	0.87[ASN][1000 genomes]
rs6441028	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66509404	0.96[ASN][1000 genomes]
rs6804740	0.85[JPT][hapmap]
rs6809229	0.86[JPT][hapmap]
rs7615287	0.87[YRI][hapmap]
rs7619976	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7629523	0.87[CHB][hapmap]
rs7633168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7643630	0.85[ASN][1000 genomes]
rs7651038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7652005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[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
rs6799267	SLC33A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155589800-155607000	Weak transcription	Pancreas	Pancrea
2	chr3:155590200-155608400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:155590200-155643000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:155590200-155667400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:155590800-155607200	Weak transcription	Brain Angular Gyrus	brain
6	chr3:155591000-155607200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:155591000-155611200	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:155591000-155611800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:155591200-155607800	Weak transcription	Fetal Intestine Small	intestine
10	chr3:155591200-155612600	Weak transcription	Primary B cells from cord blood	blood
11	chr3:155591400-155602200	Weak transcription	Fetal Lung	lung
12	chr3:155591400-155606600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:155591400-155611200	Weak transcription	Fetal Thymus	thymus
14	chr3:155591400-155616200	Weak transcription	NHEK	skin
15	chr3:155592000-155611800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:155592200-155607000	Weak transcription	NHDF-Ad	bronchial
17	chr3:155592200-155607200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:155592600-155608400	Weak transcription	Hela-S3	cervix
19	chr3:155593200-155607000	Weak transcription	Aorta	Aorta
20	chr3:155593200-155607000	Weak transcription	Psoas Muscle	Psoas
21	chr3:155593400-155607000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:155593400-155607000	Weak transcription	Gastric	stomach
23	chr3:155594200-155622000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:155594400-155607200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:155594400-155607800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:155594600-155606600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:155596800-155611200	Weak transcription	Thymus	Thymus
28	chr3:155597400-155607000	Weak transcription	Lung	lung
29	chr3:155598200-155602600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:155598400-155606800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:155598400-155607200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:155598400-155607800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr3:155598600-155630000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:155598800-155608600	Weak transcription	Dnd41	blood
35	chr3:155599400-155603000	Enhancers	K562	blood
36	chr3:155599400-155616400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:155599800-155602200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr3:155599800-155602400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:155599800-155606200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:155599800-155611400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:155599800-155633400	Weak transcription	Right Ventricle	heart
42	chr3:155600000-155606200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:155600000-155606600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr3:155600000-155607000	Weak transcription	Ovary	ovary
45	chr3:155600000-155608400	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:155600000-155611200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr3:155600000-155612000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:155600200-155602200	Weak transcription	GM12878-XiMat	blood
49	chr3:155600200-155602400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:155600200-155605000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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