Variant report

Variant	rs1197703
Chromosome Location	chr15:42126435-42126436
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42125345..42127041-chr15:42137059..42139924,2	K562	blood:
2	chr15:42119169..42123691-chr15:42124459..42130624,7	MCF-7	breast:

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

Extended variants
information (count: 54 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1122884	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes]
rs11630972	0.91[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs11631051	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs11632519	1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs11634083	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11634804	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs11636523	0.82[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs1197660	0.87[CEU][hapmap]
rs1197667	0.88[CEU][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1197669	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1197671	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1197672	0.92[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1197702	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1197705	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs1201689	0.81[CEU][hapmap]
rs12906666	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs12917387	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs17677098	0.91[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap]
rs17677757	0.87[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs17678310	0.83[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs2178003	0.91[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs2925339	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs35476790	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4923917	0.96[YRI][hapmap]
rs7167078	0.91[CEU][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs8025614	0.96[YRI][hapmap]
rs8042809	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs890497	0.83[AFR][1000 genomes]
rs890503	0.90[TSI][hapmap]
rs9646193	0.91[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:24 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1197703	MAPKBP1	cis	cerebellum	SCAN
rs1197703	EHD4	cis	multi-tissue	Pritchard
rs1197703	MAPKBP1	cis	parietal	SCAN
rs1197703	SPTBN5	cis	Artery Tibial	GTEx
rs1197703	CAPN3	cis	parietal	SCAN
rs1197703	RPAP1	cis	parietal	SCAN
rs1197703	NDUFAF1	cis	parietal	SCAN
rs1197703	SPTBN5	cis	cerebellum	SCAN
rs1197703	MAPKBP1	cis	multi-tissue	Pritchard
rs1197703	SNAP23	cis	parietal	SCAN

Chromatin state (count:114 , 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	chr15:42121200-42126600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:42121200-42130400	Weak transcription	Stomach Mucosa	stomach
4	chr15:42121400-42129400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:42121400-42130400	Weak transcription	Psoas Muscle	Psoas
6	chr15:42121400-42133800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:42121400-42138200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr15:42121400-42138400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:42121400-42138400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:42121400-42138400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:42121400-42138400	Weak transcription	Primary B cells from cord blood	blood
12	chr15:42121400-42147600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr15:42121400-42147600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:42121600-42130200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr15:42121600-42134000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:42121600-42137200	Weak transcription	Osteobl	bone
17	chr15:42121600-42137400	Weak transcription	Small Intestine	intestine
18	chr15:42121600-42138600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:42121600-42141400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:42121600-42141800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr15:42121800-42136600	Weak transcription	Brain Substantia Nigra	brain
22	chr15:42121800-42140400	Weak transcription	Hela-S3	cervix
23	chr15:42122000-42133000	Weak transcription	Colon Smooth Muscle	Colon
24	chr15:42122000-42142400	Strong transcription	Fetal Stomach	stomach
25	chr15:42122000-42142600	Strong transcription	Fetal Intestine Small	intestine
26	chr15:42122200-42126600	Genic enhancers	NHEK	skin
27	chr15:42122200-42128000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:42122200-42130200	Weak transcription	Fetal Heart	heart
29	chr15:42122200-42145400	Weak transcription	HepG2	liver
30	chr15:42122400-42127400	Weak transcription	Brain Anterior Caudate	brain
31	chr15:42122400-42142600	Weak transcription	Fetal Brain Male	brain
32	chr15:42122800-42137200	Weak transcription	NHLF	lung
33	chr15:42123000-42128000	Strong transcription	Fetal Muscle Leg	muscle
34	chr15:42123200-42126800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr15:42123200-42130200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:42123400-42130800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr15:42124200-42128000	Weak transcription	HSMM	muscle
38	chr15:42124200-42142400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr15:42124400-42126600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:42124400-42130400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr15:42124400-42138000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:42124600-42126800	Enhancers	Esophagus	oesophagus
43	chr15:42124600-42127200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr15:42124600-42127200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:42124600-42128600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr15:42124800-42126600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr15:42124800-42126600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr15:42124800-42126600	Enhancers	HMEC	breast
49	chr15:42124800-42127000	Enhancers	Primary T cells fromperipheralblood	blood
50	chr15:42124800-42127000	Enhancers	Primary T helper cells PMA-I stimulated	--

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