Variant report

Variant	rs33998939
Chromosome Location	chr17:38506301-38506302
allele	C/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	NR3C1	chr17:38505838-38506337	A549	lung:	n/a	n/a
2	POLR2A	chr17:38501562-38507336	MCF-7	breast:	n/a	n/a
3	POLR2A	chr17:38506170-38508076	H1-neurons	neurons:	n/a	n/a
4	MYC	chr17:38505656-38506613	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr17:38506212-38506529	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr17:38506245-38508070	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr17:38506226-38506351	GM12878	blood:	n/a	n/a
8	POLR2A	chr17:38506121-38506443	MCF-7	breast:	n/a	n/a
9	POLR2A	chr17:38506300-38506356	MCF-7	breast:	n/a	n/a
10	POLR2A	chr17:38506090-38506483	HepG2	liver:	n/a	n/a
11	REST	chr17:38506000-38508245	H1-neurons	neurons:	n/a	chr17:38507831-38507844 chr17:38507192-38507205
12	EP300	chr17:38504141-38508523	SK-N-SH	brain:	n/a	chr17:38507615-38507631
13	NR3C1	chr17:38505808-38506302	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38472788..38480698-chr17:38493295..38509406,39	K562	blood:
2	chr17:38333764..38335887-chr17:38505691..38508093,2	MCF-7	breast:
3	chr17:38502934..38507008-chr17:38516874..38520856,4	K562	blood:
4	chr17:38504284..38506322-chr17:38572040..38575026,3	MCF-7	breast:
5	chr17:38457066..38460899-chr17:38504442..38513119,13	K562	blood:

Variant related genes	Relation type
RARA	TF binding region
ENSG00000131747	Chromatin interaction
ENSG00000266208	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000183153	Chromatin interaction
ENSG00000270145	Chromatin interaction
ENSG00000108352	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10305288	1.00[AFR][1000 genomes]
rs10305296	1.00[AFR][1000 genomes]
rs10305303	1.00[AFR][1000 genomes]
rs10512482	0.92[EUR][1000 genomes]
rs1104761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11540720	0.92[EUR][1000 genomes]
rs12103533	0.92[EUR][1000 genomes]
rs15685	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16965660	0.92[EUR][1000 genomes]
rs16965669	0.92[EUR][1000 genomes]
rs16965734	0.92[EUR][1000 genomes]
rs16965736	0.92[EUR][1000 genomes]
rs16965748	0.92[EUR][1000 genomes]
rs16965774	0.92[EUR][1000 genomes]
rs16965778	0.92[EUR][1000 genomes]
rs17557495	1.00[AFR][1000 genomes]
rs17616365	1.00[AMR][1000 genomes]
rs17616543	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17616672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17616879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17617263	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17618397	1.00[AFR][1000 genomes]
rs17678817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17678959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17678990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17679038	1.00[AFR][1000 genomes]
rs17679086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17679361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17680217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17680410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17680507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17680624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17680685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17680704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2012667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2229773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28362320	0.92[EUR][1000 genomes]
rs28362321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28526298	0.92[EUR][1000 genomes]
rs34270904	0.92[EUR][1000 genomes]
rs34300454	0.92[EUR][1000 genomes]
rs35783632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35898909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41283417	0.92[EUR][1000 genomes]
rs41283423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4134993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4134998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45612441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7214783	0.85[EUR][1000 genomes]
rs72819623	1.00[AFR][1000 genomes]
rs72819624	1.00[AFR][1000 genomes]
rs72819628	1.00[AFR][1000 genomes]
rs72819630	1.00[AFR][1000 genomes]
rs72819632	1.00[AFR][1000 genomes]
rs72819633	1.00[AFR][1000 genomes]
rs72819651	1.00[AFR][1000 genomes]
rs8067519	0.92[EUR][1000 genomes]
rs8071687	0.92[EUR][1000 genomes]
rs8077482	0.92[EUR][1000 genomes]
rs9889905	0.92[EUR][1000 genomes]
rs9891944	1.00[EUR][1000 genomes]
rs9894364	0.92[EUR][1000 genomes]
rs9894807	0.92[EUR][1000 genomes]
rs9898500	0.92[EUR][1000 genomes]
rs9899425	0.92[EUR][1000 genomes]
rs9900154	0.92[EUR][1000 genomes]
rs9903293	0.92[EUR][1000 genomes]
rs9906274	1.00[EUR][1000 genomes]
rs9909777	0.92[EUR][1000 genomes]
rs9909811	0.92[EUR][1000 genomes]
rs9910373	0.92[EUR][1000 genomes]
rs9915775	0.92[EUR][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	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1058540	chr17:38467043-38515087	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv908222	chr17:38504241-38526973	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38498000-38508000	Weak transcription	Dnd41	blood
2	chr17:38498200-38507200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr17:38500000-38507000	Enhancers	NHDF-Ad	bronchial
4	chr17:38501800-38507200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr17:38501800-38507200	Flanking Active TSS	Brain Germinal Matrix	brain
6	chr17:38502200-38506400	Enhancers	Psoas Muscle	Psoas
7	chr17:38502200-38507600	Enhancers	Fetal Thymus	thymus
8	chr17:38502400-38508400	Enhancers	Brain Angular Gyrus	brain
9	chr17:38502600-38507000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr17:38502600-38507800	Enhancers	Fetal Heart	heart
11	chr17:38502800-38508000	Enhancers	Stomach Mucosa	stomach
12	chr17:38502800-38509400	Genic enhancers	Fetal Stomach	stomach
13	chr17:38503200-38507200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr17:38503200-38508600	Genic enhancers	NHLF	lung
15	chr17:38503200-38512600	Genic enhancers	Spleen	Spleen
16	chr17:38503400-38506400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
17	chr17:38503400-38509400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr17:38503400-38509600	Genic enhancers	Fetal Intestine Large	intestine
19	chr17:38503600-38506400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr17:38503600-38513000	Genic enhancers	A549	lung
21	chr17:38503800-38507600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr17:38503800-38508600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr17:38503800-38513600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr17:38504000-38506800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:38504000-38509400	Genic enhancers	Fetal Intestine Small	intestine
26	chr17:38504000-38511600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
27	chr17:38504000-38511600	Weak transcription	Hela-S3	cervix
28	chr17:38504200-38507200	Genic enhancers	Primary T cells fromperipheralblood	blood
29	chr17:38504200-38507200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr17:38504200-38507400	Flanking Active TSS	Fetal Brain Female	brain
31	chr17:38504200-38507800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr17:38504400-38506600	Genic enhancers	Monocytes-CD14+_RO01746	blood
33	chr17:38504400-38507000	Genic enhancers	Gastric	stomach
34	chr17:38504400-38507400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
35	chr17:38504400-38509600	Genic enhancers	Lung	lung
36	chr17:38504400-38509800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr17:38504400-38514000	Genic enhancers	Fetal Muscle Trunk	muscle
38	chr17:38504400-38514200	Genic enhancers	Fetal Muscle Leg	muscle
39	chr17:38504600-38506400	Genic enhancers	Pancreas	Pancrea
40	chr17:38504600-38506600	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
41	chr17:38504600-38506600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
42	chr17:38504600-38506800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr17:38504600-38506800	Genic enhancers	Rectal Mucosa Donor 29	rectum
44	chr17:38504600-38506800	Genic enhancers	Rectal Mucosa Donor 31	rectum
45	chr17:38504600-38507000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
46	chr17:38504600-38507200	Genic enhancers	Primary hematopoietic stem cells	blood
47	chr17:38504600-38508600	Enhancers	Brain Cingulate Gyrus	brain
48	chr17:38504600-38508600	Strong transcription	GM12878-XiMat	blood
49	chr17:38504600-38509000	Genic enhancers	Muscle Satellite Cultured Cells	--
50	chr17:38504600-38511400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood

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