Variant report

Variant	rs7636204
Chromosome Location	chr3:52013242-52013243
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	POLR2A	chr3:52013083-52013437	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:52013027-52013336	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:52013091-52013406	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:52012635-52013475	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ABHD14B	TF binding region
ACY1	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs178918	1.00[AMR][1000 genomes]
rs323869	1.00[AMR][1000 genomes]
rs323870	1.00[AMR][1000 genomes]
rs323872	0.88[LWK][hapmap];1.00[MKK][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323878	0.81[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323880	1.00[AMR][1000 genomes]
rs323889	0.96[LWK][hapmap];0.96[MKK][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323891	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323896	1.00[AMR][1000 genomes]
rs323900	0.96[LWK][hapmap];0.96[MKK][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs368210	1.00[AMR][1000 genomes]
rs422304	1.00[AMR][1000 genomes]
rs56746340	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57384151	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6446141	1.00[AMR][1000 genomes]
rs72961930	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72961999	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72964016	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7426999	0.84[LWK][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs9683234	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv876782	chr3:51985664-52022779	Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
11	nsv876784	chr3:51987224-52013242	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv876785	chr3:51994881-52022779	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
13	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52009800-52014400	Weak transcription	Ovary	ovary
2	chr3:52009800-52016400	Weak transcription	Small Intestine	intestine
3	chr3:52010000-52014200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:52010000-52014400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:52010000-52014400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:52010000-52014600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:52010000-52014800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:52010000-52014800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:52010000-52015000	Weak transcription	Hela-S3	cervix
10	chr3:52010000-52015000	Weak transcription	HepG2	liver
11	chr3:52010000-52016400	Weak transcription	Left Ventricle	heart
12	chr3:52010000-52016400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:52010000-52016400	Weak transcription	Psoas Muscle	Psoas
14	chr3:52010000-52016400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:52010000-52016400	Weak transcription	HSMMtube	muscle
16	chr3:52010000-52016400	Weak transcription	NHDF-Ad	bronchial
17	chr3:52010200-52014200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:52010200-52014200	Weak transcription	Fetal Intestine Large	intestine
19	chr3:52010200-52014200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:52010200-52014400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:52010200-52014400	Weak transcription	Fetal Lung	lung
22	chr3:52010200-52014400	Weak transcription	Gastric	stomach
23	chr3:52010200-52014400	Weak transcription	Pancreas	Pancrea
24	chr3:52010200-52014400	Weak transcription	Right Ventricle	heart
25	chr3:52010200-52014400	Weak transcription	Dnd41	blood
26	chr3:52010200-52014600	Weak transcription	Right Atrium	heart
27	chr3:52010200-52014800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:52010200-52014800	Weak transcription	Stomach Mucosa	stomach
29	chr3:52010200-52015000	Weak transcription	Colonic Mucosa	Colon
30	chr3:52010200-52015000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:52010200-52016000	Weak transcription	Primary B cells from cord blood	blood
32	chr3:52010200-52016200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:52010200-52016200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:52010200-52016200	Weak transcription	Colon Smooth Muscle	Colon
35	chr3:52010200-52016200	Weak transcription	GM12878-XiMat	blood
36	chr3:52010200-52016400	Weak transcription	HSMM	muscle
37	chr3:52010200-52016400	Weak transcription	NH-A	brain
38	chr3:52010200-52016600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:52010400-52014200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:52010400-52014200	Weak transcription	Brain Substantia Nigra	brain
41	chr3:52010400-52014200	Weak transcription	Thymus	Thymus
42	chr3:52010400-52014400	Weak transcription	Primary T cells from cord blood	blood
43	chr3:52010400-52014400	Weak transcription	Adipose Nuclei	Adipose
44	chr3:52010400-52014400	Weak transcription	Brain Angular Gyrus	brain
45	chr3:52010400-52014400	Weak transcription	Lung	lung
46	chr3:52010400-52014400	Weak transcription	NHLF	lung
47	chr3:52010400-52015200	Weak transcription	Placenta	Placenta
48	chr3:52010400-52016000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr3:52010400-52016200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:52010400-52016200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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