Variant report

Variant	rs2412640
Chromosome Location	chr15:42124082-42124083
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42122872..42126047-chr15:42126791..42131021,4	K562	blood:
2	chr15:42121774..42125537-chr15:42128092..42132193,4	MCF-7	breast:
3	chr15:42119641..42122495-chr15:42123255..42125312,3	K562	blood:

Variant related genes	Relation type
ENSG00000243708	Chromatin interaction
ENSG00000168970	Chromatin interaction
ENSG00000243789	Chromatin interaction
ENSG00000250379	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1043627	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs1106934	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs11070349	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11547012	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11630242	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1197659	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1197662	0.80[CHB][hapmap]
rs1197668	0.88[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1197687	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1197688	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs1197689	0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1197690	0.90[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1197773	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1206842	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs1209333	0.90[ASN][1000 genomes]
rs12439771	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap]
rs12440605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12591285	0.95[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs12595271	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs12901742	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs1726915	0.90[ASN][1000 genomes]
rs1918312	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs1918313	0.95[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap]
rs2077361	0.95[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap]
rs2077543	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2241523	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2577949	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs28671571	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2925340	0.89[ASN][1000 genomes]
rs35359048	0.82[ASN][1000 genomes]
rs3816533	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4923907	0.95[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap]
rs4923913	0.89[ASN][1000 genomes]
rs4923917	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924573	1.00[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs7166139	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7173779	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7174099	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7175346	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7177495	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs8025614	0.85[CEU][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs883329	0.84[ASN][1000 genomes]
rs890504	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv904115	chr15:42076387-42171483	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv904116	chr15:42076387-42229852	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
5	nsv1038393	chr15:42083574-42188035	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	esv1827003	chr15:42087505-42199076	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
7	esv1816120	chr15:42093384-42171578	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
8	nsv1041645	chr15:42095168-42186482	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1051200	chr15:42095168-42188035	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
10	nsv517631	chr15:42096926-42187492	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
11	nsv1051733	chr15:42098896-42186482	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
12	nsv1036153	chr15:42098896-42188035	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
13	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
14	nsv1048606	chr15:42101694-42192760	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
15	nsv904117	chr15:42103822-42184794	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
16	nsv904118	chr15:42103822-42207905	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
17	nsv904119	chr15:42109975-42142912	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
18	nsv904120	chr15:42109975-42153085	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer 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	17 gene(s)	inside rSNPs	diseases
19	nsv904121	chr15:42109975-42162957	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
20	nsv904122	chr15:42109975-42166475	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
21	nsv904123	chr15:42109975-42171483	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
22	nsv904124	chr15:42109975-42207905	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
23	nsv9244	chr15:42110712-42208805	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
24	nsv904125	chr15:42119900-42210393	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
25	nsv977704	chr15:42123613-42125024	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2412640	RPAP1	cis	parietal	SCAN
rs2412640	MAPKBP1	cis	cerebellum	SCAN
rs2412640	NDUFAF1	cis	parietal	SCAN
rs2412640	SNAP23	cis	parietal	SCAN
rs2412640	JMJD7-PLA2G4B	cis	parietal	SCAN
rs2412640	RPAP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42121000-42147400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:42121200-42124200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr15:42121200-42124200	Enhancers	Fetal Thymus	thymus
4	chr15:42121200-42124400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr15:42121200-42124400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:42121200-42124400	Weak transcription	Right Atrium	heart
7	chr15:42121200-42126000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr15:42121200-42126600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr15:42121200-42130400	Weak transcription	Stomach Mucosa	stomach
10	chr15:42121400-42124200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:42121400-42124200	Weak transcription	Aorta	Aorta
12	chr15:42121400-42124200	Enhancers	Dnd41	blood
13	chr15:42121400-42124600	Weak transcription	HSMMtube	muscle
14	chr15:42121400-42124800	Weak transcription	K562	blood
15	chr15:42121400-42125200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:42121400-42125400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:42121400-42125400	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr15:42121400-42126200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr15:42121400-42126200	Weak transcription	Ovary	ovary
20	chr15:42121400-42129400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr15:42121400-42130400	Weak transcription	Psoas Muscle	Psoas
22	chr15:42121400-42133800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr15:42121400-42138200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr15:42121400-42138400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:42121400-42138400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:42121400-42138400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr15:42121400-42138400	Weak transcription	Primary B cells from cord blood	blood
28	chr15:42121400-42147600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr15:42121400-42147600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr15:42121600-42124400	Weak transcription	Placenta	Placenta
31	chr15:42121600-42125400	Weak transcription	Fetal Kidney	kidney
32	chr15:42121600-42130200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr15:42121600-42134000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:42121600-42137200	Weak transcription	Osteobl	bone
35	chr15:42121600-42137400	Weak transcription	Small Intestine	intestine
36	chr15:42121600-42138600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr15:42121600-42141400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:42121600-42141800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr15:42121800-42136600	Weak transcription	Brain Substantia Nigra	brain
40	chr15:42121800-42140400	Weak transcription	Hela-S3	cervix
41	chr15:42122000-42124600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:42122000-42124800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:42122000-42124800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:42122000-42124800	Genic enhancers	Primary T cells fromperipheralblood	blood
45	chr15:42122000-42125000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:42122000-42125000	Genic enhancers	Lung	lung
47	chr15:42122000-42125000	Genic enhancers	Right Ventricle	heart
48	chr15:42122000-42125000	Genic enhancers	Spleen	Spleen
49	chr15:42122000-42125200	Genic enhancers	Pancreas	Pancrea
50	chr15:42122000-42125200	Strong transcription	Skeletal Muscle Male	skeletal muscle

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