Variant report

Variant	rs1143774
Chromosome Location	chr3:100475568-100475569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100474203..100477439-chr3:100482116..100484278,3	K562	blood:
2	chr3:100473925..100475796-chr3:100476025..100478809,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10755119	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[TSI][hapmap];1.00[ASN][1000 genomes]
rs10936349	0.85[EUR][1000 genomes]
rs11353	0.85[EUR][1000 genomes]
rs1143776	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1144105	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144106	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144107	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144108	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144122	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs1144124	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1144125	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs1144126	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[TSI][hapmap];1.00[ASN][1000 genomes]
rs1145348	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1145351	1.00[ASN][1000 genomes]
rs1165253	1.00[ASN][1000 genomes]
rs1165255	1.00[ASN][1000 genomes]
rs1165260	1.00[ASN][1000 genomes]
rs1165264	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1165534	1.00[ASN][1000 genomes]
rs11921801	1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs11921907	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1384198	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs1520652	1.00[ASN][1000 genomes]
rs1620897	1.00[ASN][1000 genomes]
rs1623413	1.00[ASN][1000 genomes]
rs1676339	1.00[ASN][1000 genomes]
rs1676343	1.00[CHB][hapmap]
rs1676345	1.00[ASN][1000 genomes]
rs1676346	1.00[ASN][1000 genomes]
rs1676349	1.00[ASN][1000 genomes]
rs1676366	1.00[ASN][1000 genomes]
rs1680520	1.00[ASN][1000 genomes]
rs1718272	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1718273	1.00[ASN][1000 genomes]
rs1718278	1.00[ASN][1000 genomes]
rs1718279	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1915309	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2126540	0.83[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2461498	1.00[ASN][1000 genomes]
rs3087787	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3796276	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4088588	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4144968	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4367102	0.81[EUR][1000 genomes]
rs4928070	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs4928081	0.81[EUR][1000 genomes]
rs560803	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586347	1.00[CHB][hapmap]
rs591728	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603630	1.00[ASN][1000 genomes]
rs605300	1.00[ASN][1000 genomes]
rs610854	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs629091	1.00[ASN][1000 genomes]
rs6441383	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6441384	1.00[CHB][hapmap]
rs653002	1.00[ASN][1000 genomes]
rs670008	1.00[CHB][hapmap]
rs6767460	1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770559	1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773482	0.80[EUR][1000 genomes]
rs6779489	1.00[CHB][hapmap]
rs6788891	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs6789364	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6798180	0.82[EUR][1000 genomes]
rs694612	1.00[ASN][1000 genomes]
rs7617579	0.81[EUR][1000 genomes]
rs7627660	0.81[EUR][1000 genomes]
rs7635652	0.82[EUR][1000 genomes]
rs7637250	0.82[EUR][1000 genomes]
rs7637272	0.82[EUR][1000 genomes]
rs7644599	1.00[ASN][1000 genomes]
rs900234	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9843956	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9864288	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9878163	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751968	chr3:100299329-100476713	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv432466	chr3:100299329-100476713	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv2751969	chr3:100312499-100479384	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv2751972	chr3:100342493-100493062	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv432469	chr3:100342493-100493062	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	esv2751973	chr3:100354170-100476713	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv2751974	chr3:100354170-100476713	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1143774	TFG	cis	multi-tissue	Pritchard
rs1143774	ST3GAL6	cis	parietal	SCAN
rs1143774	TMEM45A	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100434400-100478200	Weak transcription	Spleen	Spleen
2	chr3:100441000-100479400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:100445400-100475600	Weak transcription	Pancreas	Pancrea
4	chr3:100447600-100477200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:100450000-100501000	Weak transcription	Esophagus	oesophagus
6	chr3:100453200-100479000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:100457200-100480200	Weak transcription	Brain Angular Gyrus	brain
8	chr3:100459400-100478200	Weak transcription	Fetal Stomach	stomach
9	chr3:100465600-100478000	Weak transcription	Aorta	Aorta
10	chr3:100465600-100478000	Weak transcription	Fetal Heart	heart
11	chr3:100467400-100475800	Weak transcription	Thymus	Thymus
12	chr3:100467400-100497600	Weak transcription	Fetal Intestine Small	intestine
13	chr3:100468200-100488600	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:100469000-100475800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:100469400-100480200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:100469600-100479200	Weak transcription	Fetal Brain Male	brain
17	chr3:100469800-100477600	Weak transcription	K562	blood
18	chr3:100469800-100498200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:100469800-100501400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:100470200-100498400	Weak transcription	Right Ventricle	heart
21	chr3:100471000-100476000	Weak transcription	HUVEC	blood vessel
22	chr3:100471000-100477600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:100471000-100495800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:100471200-100478200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:100471200-100480200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:100471600-100475600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:100471600-100478400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:100471600-100500400	Weak transcription	Lung	lung
29	chr3:100471800-100475800	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:100471800-100479400	Weak transcription	Fetal Kidney	kidney
31	chr3:100471800-100486200	Weak transcription	Brain Substantia Nigra	brain
32	chr3:100471800-100494600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:100471800-100502000	Weak transcription	Brain Anterior Caudate	brain
34	chr3:100472000-100475800	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr3:100472200-100476000	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr3:100472600-100475800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:100472600-100484600	Weak transcription	NHEK	skin
38	chr3:100472800-100475600	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr3:100472800-100476600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:100472800-100478200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr3:100472800-100482800	Weak transcription	NHLF	lung
42	chr3:100472800-100494400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:100473000-100475800	Weak transcription	Fetal Thymus	thymus
44	chr3:100473000-100478200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:100473000-100479800	Weak transcription	GM12878-XiMat	blood
46	chr3:100473000-100480400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:100473200-100478000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:100473400-100480200	Weak transcription	A549	lung
49	chr3:100473400-100488400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr3:100473600-100475800	Weak transcription	Rectal Mucosa Donor 31	rectum

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