Variant report

Variant	rs11070349
Chromosome Location	chr15:42085017-42085018
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42067373..42071061-chr15:42083349..42086299,3	K562	blood:
2	chr15:42084827..42086940-chr15:42091346..42094330,2	K562	blood:

Variant related genes	Relation type
ENSG00000137802	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1043627	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1106934	0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11070346	0.83[ASN][1000 genomes]
rs11547012	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11630242	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11853665	0.82[ASN][1000 genomes]
rs11858843	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1197659	0.95[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1197662	0.87[CHB][hapmap]
rs1197668	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1197687	0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1197688	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1197689	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs1197690	0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1197770	0.82[ASN][1000 genomes]
rs1197773	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1206842	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1209333	0.94[ASN][1000 genomes]
rs12439771	0.95[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs12440605	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12591285	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs12595271	0.95[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs12901742	0.95[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs16971915	0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs1726915	0.94[ASN][1000 genomes]
rs1918312	0.95[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1918313	0.90[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2077361	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2077543	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2241523	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2412640	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]
rs2577949	0.95[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs28671571	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2925340	0.93[ASN][1000 genomes]
rs34769385	0.82[ASN][1000 genomes]
rs35033220	0.83[ASN][1000 genomes]
rs35359048	0.86[ASN][1000 genomes]
rs3816533	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4072386	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4923906	0.82[ASN][1000 genomes]
rs4923907	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs4923913	0.93[ASN][1000 genomes]
rs4923917	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs4924573	1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs7166139	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7168489	0.83[ASN][1000 genomes]
rs7173779	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7174099	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7175346	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7177495	0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs8025614	0.85[CEU][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap]
rs883329	0.80[ASN][1000 genomes]
rs890504	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9806709	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11070349	MAPKBP1	cis	cerebellum	SCAN
rs11070349	RPAP1	cis	lymphoblastoid	seeQTL
rs11070349	NDUFAF1	cis	parietal	SCAN
rs11070349	SNAP23	cis	parietal	SCAN
rs11070349	MAPKBP1	cis	parietal	SCAN
rs11070349	RPAP1	cis	parietal	SCAN
rs11070349	JMJD7-PLA2G4B	cis	parietal	SCAN

Chromatin state (count:109 , 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	chr15:42079000-42085200	Enhancers	Fetal Intestine Large	intestine
5	chr15:42079200-42090000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:42079800-42089000	Enhancers	HMEC	breast
7	chr15:42080600-42085200	Enhancers	Left Ventricle	heart
8	chr15:42080600-42086600	Enhancers	Ovary	ovary
9	chr15:42080600-42086800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:42080600-42088200	Enhancers	NHDF-Ad	bronchial
11	chr15:42081000-42091800	Enhancers	Placenta	Placenta
12	chr15:42081200-42085200	Enhancers	Psoas Muscle	Psoas
13	chr15:42081600-42085600	Enhancers	Fetal Muscle Leg	muscle
14	chr15:42081600-42087200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:42081800-42086600	Enhancers	K562	blood
16	chr15:42081800-42092400	Weak transcription	Fetal Brain Female	brain
17	chr15:42082400-42086400	Enhancers	Fetal Heart	heart
18	chr15:42082400-42088800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:42082600-42092000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr15:42082800-42092400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:42083400-42085800	Weak transcription	Brain Angular Gyrus	brain
22	chr15:42083400-42091000	Weak transcription	Fetal Stomach	stomach
23	chr15:42083400-42092000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr15:42083600-42085200	Genic enhancers	Fetal Intestine Small	intestine
25	chr15:42083600-42085200	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr15:42083600-42085400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:42083600-42089400	Weak transcription	Small Intestine	intestine
28	chr15:42083600-42104600	Weak transcription	Liver	Liver
29	chr15:42083600-42109200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:42083800-42087200	Genic enhancers	NHEK	skin
31	chr15:42083800-42088000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:42083800-42088200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr15:42083800-42088200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:42083800-42088400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr15:42083800-42088800	Weak transcription	Aorta	Aorta
36	chr15:42083800-42089200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr15:42083800-42096600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr15:42083800-42098600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:42083800-42098600	Weak transcription	Pancreas	Pancrea
40	chr15:42083800-42098600	Weak transcription	A549	lung
41	chr15:42083800-42103200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr15:42083800-42103400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr15:42083800-42104400	Weak transcription	Colonic Mucosa	Colon
44	chr15:42083800-42105000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr15:42083800-42119400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr15:42084000-42085400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:42084000-42085400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr15:42084000-42085400	Enhancers	HUVEC	blood vessel
49	chr15:42084000-42085800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr15:42084000-42085800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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