Variant report

Variant	rs10804774
Chromosome Location	chr3:155654017-155654018
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:155608624..155610352-chr3:155653866..155656190,2	K562	blood:
2	chr3:155626966..155628913-chr3:155652497..155654846,2	K562	blood:
3	chr3:155523032..155525665-chr3:155651721..155654072,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174928	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10804773	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10936020	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1131925	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11714133	0.94[ASN][1000 genomes]
rs13059611	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13091683	0.91[ASN][1000 genomes]
rs2054878	0.90[ASN][1000 genomes]
rs2063903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2200707	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs34337666	0.87[ASN][1000 genomes]
rs35321137	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35472369	0.90[ASN][1000 genomes]
rs358703	0.87[MEX][hapmap]
rs3772115	0.99[ASN][1000 genomes]
rs3772116	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3821365	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680219	0.95[ASN][1000 genomes]
rs4680223	0.96[ASN][1000 genomes]
rs6441028	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66509404	0.92[ASN][1000 genomes]
rs6763830	0.87[ASN][1000 genomes]
rs6799267	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]
rs6804740	0.90[JPT][hapmap]
rs6809229	0.86[JPT][hapmap]
rs7615287	0.89[YRI][hapmap]
rs7619976	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7629523	0.86[CHB][hapmap]
rs7633168	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7643630	0.82[ASN][1000 genomes]
rs7651038	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7652005	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10804774	SLC33A1	Cis_1M	lymphoblastoid	RTeQTL
rs10804774	PLCH1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155590200-155667400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:155603800-155657800	Weak transcription	Esophagus	oesophagus
3	chr3:155604400-155658600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:155607200-155656800	Weak transcription	Small Intestine	intestine
5	chr3:155607400-155669000	Weak transcription	Pancreas	Pancrea
6	chr3:155608800-155654800	Weak transcription	Aorta	Aorta
7	chr3:155609200-155657200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:155633800-155668200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:155634200-155654600	Weak transcription	Spleen	Spleen
10	chr3:155634400-155654200	Weak transcription	Colonic Mucosa	Colon
11	chr3:155634600-155656200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:155634600-155660600	Weak transcription	Stomach Mucosa	stomach
13	chr3:155635800-155654400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:155635800-155658000	Weak transcription	Fetal Kidney	kidney
15	chr3:155635800-155664400	Weak transcription	Gastric	stomach
16	chr3:155638000-155654600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:155639600-155654600	Weak transcription	Psoas Muscle	Psoas
18	chr3:155639600-155664400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:155639600-155671000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:155644000-155654600	Weak transcription	Fetal Brain Male	brain
21	chr3:155644000-155654800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:155644000-155657200	Weak transcription	Right Ventricle	heart
23	chr3:155644000-155663600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:155644000-155666800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:155644200-155659800	Weak transcription	Brain Angular Gyrus	brain
26	chr3:155644200-155662000	Weak transcription	Brain Germinal Matrix	brain
27	chr3:155644200-155665200	Weak transcription	Fetal Stomach	stomach
28	chr3:155646200-155665200	Weak transcription	Fetal Intestine Small	intestine
29	chr3:155648400-155658000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:155648400-155661800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:155648400-155663000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:155648600-155656200	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:155648600-155658600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:155648600-155659400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:155648600-155659600	Strong transcription	Fetal Thymus	thymus
36	chr3:155648600-155659800	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:155648600-155659800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:155648600-155661000	Strong transcription	Dnd41	blood
39	chr3:155649000-155667400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:155649400-155656000	Strong transcription	K562	blood
41	chr3:155649400-155656800	Strong transcription	NH-A	brain
42	chr3:155649400-155658600	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:155649600-155656600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:155649600-155657000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:155649600-155657000	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr3:155649600-155657200	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr3:155649600-155658200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr3:155649600-155658800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:155649600-155658800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:155649600-155659800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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