Variant report

Variant	rs3743102
Chromosome Location	chr15:83427394-83427395
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83417813..83422044-chr15:83423321..83428058,7	MCF-7	breast:
2	chr15:83425158..83429162-chr15:83434771..83437129,3	K562	blood:
3	chr15:83422361..83425357-chr15:83426199..83428085,2	MCF-7	breast:
4	chr15:83417439..83419471-chr15:83427262..83430015,3	MCF-7	breast:
5	chr15:83422082..83425178-chr15:83425746..83427952,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250988	Chromatin interaction
ENSG00000252690	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1124911	0.92[CEU][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.88[MKK][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28540813	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28664062	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28847707	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3803383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4638544	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4779062	0.83[ASN][1000 genomes]
rs7174656	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8023873	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1036950	chr15:83245326-83461261	Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv34318	chr15:83283555-83453495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1039021	chr15:83283994-83431548	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3493740	chr15:83295897-83458896	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	esv3493739	chr15:83296247-83458846	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	esv3493738	chr15:83296905-83457854	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	esv3493742	chr15:83296993-83457792	Weak transcription Active TSS Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv817702	chr15:83299461-83457424	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv469557	chr15:83417763-83560629	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv482340	chr15:83417763-83560629	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv471687	chr15:83417764-83560629	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
14	esv3346074	chr15:83422947-83456222	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3743102	HDGFRP3	cis	parietal	SCAN
rs3743102	CTSH	cis	parietal	SCAN
rs3743102	RASGRF1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83420200-83433400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:83420400-83436400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:83420600-83429000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:83420800-83431400	Weak transcription	Stomach Mucosa	stomach
5	chr15:83421000-83428000	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:83421000-83428200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:83421000-83428400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:83421000-83428400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:83421000-83428600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr15:83421000-83429400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:83421200-83428200	Strong transcription	Fetal Thymus	thymus
12	chr15:83421200-83430000	Strong transcription	Primary hematopoietic stem cells	blood
13	chr15:83421200-83431200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:83421200-83431200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:83421200-83431600	Strong transcription	Duodenum Mucosa	Duodenum
16	chr15:83421200-83432000	Strong transcription	A549	lung
17	chr15:83421400-83428200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:83421400-83428200	Strong transcription	HUVEC	blood vessel
19	chr15:83421400-83428400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr15:83421400-83431400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:83421400-83431600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:83421600-83428200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr15:83421600-83431200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:83421600-83431600	Strong transcription	Adipose Nuclei	Adipose
25	chr15:83421600-83432800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr15:83421800-83427600	Strong transcription	Fetal Muscle Leg	muscle
27	chr15:83422000-83428200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:83422000-83430600	Weak transcription	Small Intestine	intestine
29	chr15:83422000-83431400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr15:83422000-83431600	Strong transcription	Liver	Liver
31	chr15:83422200-83429800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr15:83422200-83431200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:83422200-83431600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:83422200-83435200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr15:83422400-83428400	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr15:83422400-83436800	Strong transcription	Primary T cells from cord blood	blood
37	chr15:83422600-83428200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:83422800-83428200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr15:83422800-83428200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr15:83422800-83430000	Strong transcription	Primary B cells from peripheral blood	blood
41	chr15:83422800-83430000	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr15:83422800-83430400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:83423000-83428000	Strong transcription	Primary B cells from cord blood	blood
44	chr15:83423000-83428000	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr15:83423000-83428200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:83423200-83427800	Strong transcription	Osteobl	bone
47	chr15:83423200-83428000	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr15:83423200-83428400	Strong transcription	Placenta	Placenta
49	chr15:83423200-83429600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr15:83423200-83431600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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