Variant report

Variant	rs7516436
Chromosome Location	chr1:213187759-213187760
allele	A/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	chr1:213187368-213189944	K562	blood:	n/a	n/a
2	POLR2A	chr1:213187556-213189480	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:213187027-213189329	K562	blood:	n/a	n/a
4	HCFC1	chr1:213187601-213189893	Hela-S3	cervix:	n/a	n/a
5	RFX5	chr1:213187621-213188188	K562	blood:	n/a	n/a
6	MYC	chr1:213187649-213188538	MCF10A-Er-Src	breast:	n/a	chr1:213188520-213188536
7	POLR2A	chr1:213187055-213189320	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:213187275-213189486	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212780951..212783989-chr1:213187661..213190726,3	K562	blood:
2	chr1:213030101..213032938-chr1:213186047..213190102,3	K562	blood:

Variant related genes	Relation type
ANGEL2	TF binding region
ENSG00000162769	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000198468	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10157273	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11120082	0.85[YRI][hapmap]
rs11810428	1.00[EUR][1000 genomes]
rs41277158	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6540771	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6540772	0.80[EUR][1000 genomes]
rs6540775	0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs6688043	0.80[EUR][1000 genomes]
rs6692011	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6694156	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6697921	0.85[YRI][hapmap]
rs7520067	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7525940	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008594	chr1:213110654-213236750	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213154800-213188000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:213154800-213188400	Weak transcription	Spleen	Spleen
3	chr1:213155600-213188000	Weak transcription	Aorta	Aorta
4	chr1:213155600-213188000	Weak transcription	Esophagus	oesophagus
5	chr1:213156200-213188000	Weak transcription	Pancreas	Pancrea
6	chr1:213158400-213188000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:213160200-213188000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:213162200-213188000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:213167800-213187800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:213169000-213187800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:213170000-213188000	Weak transcription	Colonic Mucosa	Colon
12	chr1:213170600-213187800	Weak transcription	Fetal Kidney	kidney
13	chr1:213177400-213187800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:213177400-213188000	Weak transcription	Lung	lung
15	chr1:213178600-213188400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:213178800-213188000	Weak transcription	Gastric	stomach
17	chr1:213179600-213187800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:213180200-213188000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:213180400-213188000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:213180400-213188000	Weak transcription	Fetal Stomach	stomach
21	chr1:213181600-213188000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:213181800-213187800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:213182200-213188000	Weak transcription	Fetal Intestine Large	intestine
24	chr1:213182200-213188000	Weak transcription	Ovary	ovary
25	chr1:213184600-213188000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:213185200-213188000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:213185600-213187800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:213185600-213187800	Weak transcription	HSMMtube	muscle
29	chr1:213185600-213188000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:213185600-213188000	Weak transcription	Placenta	Placenta
31	chr1:213185800-213187800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr1:213185800-213187800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:213186000-213188000	Weak transcription	Fetal Thymus	thymus
34	chr1:213186400-213187800	Enhancers	Brain Cingulate Gyrus	brain
35	chr1:213186400-213187800	Enhancers	HepG2	liver
36	chr1:213186400-213188000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr1:213186600-213187800	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr1:213186800-213187800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:213186800-213187800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:213186800-213187800	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr1:213186800-213187800	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr1:213186800-213187800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:213186800-213188000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:213186800-213188000	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr1:213186800-213188000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:213186800-213188000	Weak transcription	Fetal Muscle Leg	muscle
47	chr1:213186800-213188000	Weak transcription	Left Ventricle	heart
48	chr1:213186800-213188000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr1:213186800-213188000	Weak transcription	HSMM	muscle
50	chr1:213186800-213189800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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