Variant report

Variant	rs11636944
Chromosome Location	chr15:99647605-99647606
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:99644995-99647972	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99647277..99649592-chr15:99649825..99652713,2	K562	blood:
2	chr15:99647521..99649996-chr15:99837108..99838795,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259475	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11014	0.89[EUR][1000 genomes]
rs12439693	0.87[MEX][hapmap]
rs12440758	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs12440983	0.89[ASN][1000 genomes]
rs1670267	0.83[ASN][1000 genomes]
rs1670268	0.83[ASN][1000 genomes]
rs1703796	0.83[ASN][1000 genomes]
rs1703797	0.83[ASN][1000 genomes]
rs2312484	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs260097	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs260098	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs260099	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs260100	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs260112	0.84[GIH][hapmap]
rs2602024	0.84[GIH][hapmap]
rs35049808	0.89[ASN][1000 genomes]
rs6598223	0.89[ASN][1000 genomes]
rs8028199	0.84[ASN][1000 genomes]
rs8028233	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8033198	0.89[ASN][1000 genomes]
rs8036962	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv533375	chr15:99443534-99696221	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1050982	chr15:99450004-99725825	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv530685	chr15:99452377-99713365	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
13	nsv904544	chr15:99524865-99655744	Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
15	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
17	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
19	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11636944	ALDH1A3	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99645000-99648000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
2	chr15:99645000-99648200	Active TSS	Right Atrium	heart
3	chr15:99645000-99649600	Active TSS	Rectal Smooth Muscle	rectum
4	chr15:99645200-99648200	Active TSS	Psoas Muscle	Psoas
5	chr15:99645200-99648400	Active TSS	Colon Smooth Muscle	Colon
6	chr15:99646000-99648000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr15:99646000-99648000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
8	chr15:99646200-99648000	Enhancers	HepG2	liver
9	chr15:99646200-99648200	Flanking Active TSS	Hela-S3	cervix
10	chr15:99646400-99648200	Flanking Active TSS	Brain Substantia Nigra	brain
11	chr15:99646400-99663200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:99646600-99647800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
13	chr15:99646600-99647800	Flanking Active TSS	A549	lung
14	chr15:99646600-99648000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:99646600-99648000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
16	chr15:99646600-99648000	Enhancers	Liver	Liver
17	chr15:99646600-99648000	Active TSS	Right Ventricle	heart
18	chr15:99646600-99653800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:99646600-99662200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:99646800-99647800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:99646800-99647800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:99646800-99647800	Enhancers	Placenta	Placenta
23	chr15:99646800-99647800	Active TSS	Osteobl	bone
24	chr15:99646800-99648000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr15:99646800-99648000	Flanking Active TSS	Brain Angular Gyrus	brain
26	chr15:99646800-99648000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
27	chr15:99646800-99648200	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr15:99646800-99663600	Weak transcription	Ovary	ovary
29	chr15:99646800-99663600	Weak transcription	Spleen	Spleen
30	chr15:99647000-99649800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:99647000-99662000	Weak transcription	HUVEC	blood vessel
32	chr15:99647000-99663200	Weak transcription	HSMM	muscle
33	chr15:99647200-99647800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:99647200-99647800	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr15:99647200-99648000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:99647200-99648000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:99647200-99648000	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
38	chr15:99647200-99648200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr15:99647200-99648200	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr15:99647200-99649200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:99647200-99654000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:99647400-99647800	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr15:99647400-99647800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
44	chr15:99647400-99648000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:99647400-99648000	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr15:99647400-99648000	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
47	chr15:99647400-99648200	Active TSS	Duodenum Mucosa	Duodenum
48	chr15:99647400-99648200	Flanking Active TSS	Left Ventricle	heart
49	chr15:99647400-99648200	Enhancers	Dnd41	blood
50	chr15:99647400-99649800	Enhancers	Fetal Heart	heart

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