Variant report

Variant	rs12576371
Chromosome Location	chr11:36184445-36184446
allele	A/G
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	NFIC	chr11:36184213-36185083	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr11:36184192-36185085	SK-N-SH	brain:	n/a	n/a
3	YY1	chr11:36184221-36184914	SK-N-SH_RA	brain:	n/a	chr11:36184345-36184361 chr11:36184346-36184356
4	EP300	chr11:36183675-36188790	SK-N-SH	brain:	n/a	chr11:36187236-36187245 chr11:36187949-36187963
5	REST	chr11:36184285-36185003	SK-N-SH	brain:	n/a	n/a
6	EP300	chr11:36184181-36185089	SK-N-SH_RA	brain:	n/a	n/a
7	TCF12	chr11:36184148-36185126	SK-N-SH	brain:	n/a	n/a
8	RAD21	chr11:36184436-36184922	SK-N-SH_RA	brain:	n/a	n/a
9	PBX3	chr11:36184317-36185056	SK-N-SH	brain:	n/a	n/a
10	PBX3	chr11:36184285-36185000	SK-N-SH	brain:	n/a	n/a
11	TCF12	chr11:36184077-36185249	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr11:36184327-36185078	SK-N-SH	brain:	n/a	n/a
13	GATA3	chr11:36184433-36185050	SH-SY5Y	brain:	n/a	n/a
14	EP300	chr11:36184215-36185142	SK-N-SH_RA	brain:	n/a	n/a
15	YY1	chr11:36184261-36184881	SK-N-SH_RA	brain:	n/a	chr11:36184345-36184361 chr11:36184346-36184356
16	GATA2	chr11:36184158-36185250	SH-SY5Y	brain:	n/a	n/a
17	GATA3	chr11:36184212-36185155	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr11:36184323-36184563	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
LDLRAD3	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1014357	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10836513	0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs10836514	0.99[ASN][1000 genomes]
rs11033473	0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs11033476	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11033477	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11033478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11499817	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12269916	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs12278757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12282945	0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs12417496	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs12417511	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs12420381	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12575549	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16926221	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35567395	0.88[ASN][1000 genomes]
rs4612777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4755439	0.82[ASN][1000 genomes]
rs4756291	0.87[ASN][1000 genomes]
rs4756292	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59459290	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6416082	0.87[ASN][1000 genomes]
rs6416083	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7117510	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs7121939	0.85[ASN][1000 genomes]
rs72935599	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72935601	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7929112	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7933303	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7943467	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7943612	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7948709	0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs7951966	0.88[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467791	chr11:36108497-36999385	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv554003	chr11:36108497-36999385	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv897225	chr11:36136912-36244190	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:36171600-36187800	Weak transcription	Spleen	Spleen
2	chr11:36172600-36190400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:36178200-36186000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:36178200-36187200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:36179200-36185600	Weak transcription	NHEK	skin
6	chr11:36179400-36185600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr11:36179400-36185800	Weak transcription	HSMM	muscle
8	chr11:36179600-36184600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:36179600-36193000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:36179800-36184600	Weak transcription	HUVEC	blood vessel
11	chr11:36181200-36187800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr11:36181200-36188000	Enhancers	Fetal Lung	lung
13	chr11:36181400-36186400	Enhancers	Fetal Muscle Leg	muscle
14	chr11:36181800-36185600	Weak transcription	Lung	lung
15	chr11:36182600-36184600	Enhancers	Psoas Muscle	Psoas
16	chr11:36183000-36187800	Enhancers	Fetal Stomach	stomach
17	chr11:36183200-36185000	Enhancers	Rectal Smooth Muscle	rectum
18	chr11:36183200-36185200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:36183200-36185400	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr11:36183200-36186400	Enhancers	HSMMtube	muscle
21	chr11:36183400-36185200	Enhancers	Brain Cingulate Gyrus	brain
22	chr11:36183400-36185400	Enhancers	Colon Smooth Muscle	Colon
23	chr11:36183400-36187800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr11:36183800-36184600	Enhancers	H1 Cell Line	embryonic stem cell
25	chr11:36183800-36184600	Enhancers	H9 Cell Line	embryonic stem cell
26	chr11:36183800-36184600	Enhancers	Placenta	Placenta
27	chr11:36183800-36185200	Enhancers	Adipose Nuclei	Adipose
28	chr11:36183800-36185600	Flanking Active TSS	Fetal Brain Female	brain
29	chr11:36183800-36185600	Enhancers	Fetal Kidney	kidney
30	chr11:36183800-36185800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr11:36183800-36185800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:36183800-36186000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:36183800-36186200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:36183800-36186400	Enhancers	Ovary	ovary
35	chr11:36184000-36184600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:36184000-36184600	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr11:36184000-36184600	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr11:36184000-36184600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr11:36184000-36184800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:36184000-36184800	Enhancers	Brain Hippocampus Middle	brain
41	chr11:36184000-36185000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:36184000-36185000	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr11:36184000-36185000	Enhancers	Left Ventricle	heart
44	chr11:36184000-36185200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:36184000-36185200	Enhancers	Brain Substantia Nigra	brain
46	chr11:36184000-36185200	Flanking Active TSS	Fetal Heart	heart
47	chr11:36184000-36185200	Enhancers	Stomach Smooth Muscle	stomach
48	chr11:36184000-36185400	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr11:36184000-36185800	Enhancers	Brain Anterior Caudate	brain
50	chr11:36184000-36186400	Flanking Active TSS	Brain Germinal Matrix	brain

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