Variant report

Variant	rs1197671
Chromosome Location	chr15:42091385-42091386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42064762..42066652-chr15:42089639..42091508,2	K562	blood:
2	chr15:42084827..42086940-chr15:42091346..42094330,2	K562	blood:
3	chr15:42090667..42093233-chr15:42097205..42099737,2	K562	blood:

Variant related genes	Relation type
ENSG00000137802	Chromatin interaction
ENSG00000260814	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1122884	0.96[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11630972	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs11631051	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11632519	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11633160	0.89[EUR][1000 genomes]
rs11634083	0.95[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs11634582	1.00[JPT][hapmap]
rs11634804	0.96[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11636523	0.86[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs1197660	0.83[CEU][hapmap]
rs1197667	0.88[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs1197669	0.83[ASW][hapmap];0.96[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes]
rs1197672	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1197702	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1197703	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]
rs1197705	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1197706	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12148570	0.81[EUR][1000 genomes]
rs12906666	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs12917387	0.91[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs17677098	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs17677757	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs17678310	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs2178003	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs2925339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34621600	0.82[EUR][1000 genomes]
rs35476790	0.89[AMR][1000 genomes]
rs35665813	0.80[EUR][1000 genomes]
rs61104950	0.81[EUR][1000 genomes]
rs62003901	0.81[EUR][1000 genomes]
rs7167078	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs7175318	0.80[EUR][1000 genomes]
rs8040094	0.81[EUR][1000 genomes]
rs8042809	0.87[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs890503	0.90[TSI][hapmap]
rs9646193	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv1036086	chr15:42004962-42091451	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers 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 target site	15 gene(s)	inside rSNPs	diseases
3	nsv1054671	chr15:42016097-42098896	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS 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	18 gene(s)	inside rSNPs	diseases
4	esv2757597	chr15:42047173-42122617	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	esv2760027	chr15:42047173-42122617	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv904113	chr15:42050390-42118971	Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription 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 target site	19 gene(s)	inside rSNPs	diseases
7	nsv904114	chr15:42050390-42119900	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1197671	CAPN3	cis	parietal	SCAN
rs1197671	MAPKBP1	cis	cerebellum	SCAN
rs1197671	SPTBN5	cis	cerebellum	SCAN
rs1197671	MAPKBP1	cis	parietal	SCAN
rs1197671	NDUFAF1	cis	parietal	SCAN
rs1197671	RPAP1	cis	parietal	SCAN
rs1197671	EHD4	cis	multi-tissue	Pritchard
rs1197671	MAPKBP1	cis	multi-tissue	Pritchard
rs1197671	SNAP23	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42070200-42109800	Weak transcription	Fetal Brain Male	brain
2	chr15:42071000-42092800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:42071200-42092000	Weak transcription	Brain Germinal Matrix	brain
4	chr15:42081000-42091800	Enhancers	Placenta	Placenta
5	chr15:42081800-42092400	Weak transcription	Fetal Brain Female	brain
6	chr15:42082600-42092000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:42082800-42092400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:42083400-42092000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:42083600-42104600	Weak transcription	Liver	Liver
10	chr15:42083600-42109200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:42083800-42096600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:42083800-42098600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:42083800-42098600	Weak transcription	Pancreas	Pancrea
14	chr15:42083800-42098600	Weak transcription	A549	lung
15	chr15:42083800-42103200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:42083800-42103400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:42083800-42104400	Weak transcription	Colonic Mucosa	Colon
18	chr15:42083800-42105000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr15:42083800-42119400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr15:42084000-42091600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:42084000-42091600	Weak transcription	Gastric	stomach
22	chr15:42084000-42098400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr15:42084800-42091600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr15:42085200-42097400	Weak transcription	Psoas Muscle	Psoas
25	chr15:42085400-42093200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr15:42086800-42092000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr15:42088200-42091800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:42088200-42092200	Enhancers	Hela-S3	cervix
29	chr15:42088400-42092000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:42088600-42091600	Weak transcription	Primary B cells from cord blood	blood
31	chr15:42088600-42091600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr15:42088600-42103000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:42088800-42091400	Weak transcription	Dnd41	blood
34	chr15:42088800-42091600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr15:42088800-42091800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr15:42088800-42092400	Enhancers	Fetal Heart	heart
37	chr15:42089000-42091800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr15:42089000-42091800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr15:42089000-42092000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr15:42089000-42096400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr15:42089400-42092800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr15:42089400-42114800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr15:42089600-42096600	Weak transcription	Brain Angular Gyrus	brain
44	chr15:42089800-42091400	Weak transcription	Stomach Mucosa	stomach
45	chr15:42089800-42091600	Weak transcription	Adipose Nuclei	Adipose
46	chr15:42089800-42094200	Strong transcription	Primary T cells from cord blood	blood
47	chr15:42089800-42096400	Weak transcription	Colon Smooth Muscle	Colon
48	chr15:42089800-42096400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr15:42089800-42096800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr15:42090000-42091400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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