Variant report

Variant	rs323878
Chromosome Location	chr3:51999847-51999848
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:51997165-51999885	K562	blood:	n/a	n/a
2	MXI1	chr3:51999719-52003632	SK-N-SH	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:51974673..51977845-chr3:51999030..52003727,6	K562	blood:
2	chr3:51996322..51998656-chr3:51999527..52001457,4	MCF-7	breast:
3	chr3:51974263..51976425-chr3:51999030..52003412,4	K562	blood:
4	chr3:51980428..51982546-chr3:51998419..52000085,2	K562	blood:
5	chr3:51997248..52000056-chr3:52000079..52001783,2	MCF-7	breast:
6	chr3:51972287..51978873-chr3:51998179..52003667,9	MCF-7	breast:
7	chr3:51966649..51968588-chr3:51999482..52001370,2	K562	blood:

No data

Variant related genes	Relation type
PCBP4	TF binding region
ENSG00000114767	Chromatin interaction
ENSG00000090097	Chromatin interaction
ENSG00000041880	Chromatin interaction

Extended variants
information (count: 34 )
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	1.00[AMR][1000 genomes]
rs323880	1.00[AMR][1000 genomes]
rs323889	0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323891	1.00[AMR][1000 genomes]
rs323896	1.00[AMR][1000 genomes]
rs323900	0.93[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs368210	1.00[AMR][1000 genomes]
rs422304	1.00[AMR][1000 genomes]
rs56746340	1.00[AMR][1000 genomes]
rs57384151	1.00[AMR][1000 genomes]
rs6446141	1.00[AMR][1000 genomes]
rs72961930	1.00[AMR][1000 genomes]
rs72961999	1.00[AMR][1000 genomes]
rs72964016	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7426999	1.00[AMR][1000 genomes]
rs7636204	0.81[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9683234	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv876781	chr3:51985664-52009612	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	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
12	nsv876783	chr3:51987224-52009612	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	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
14	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

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51988400-52000600	Weak transcription	Hela-S3	cervix
2	chr3:51990600-52000200	Weak transcription	NHDF-Ad	bronchial
3	chr3:51990600-52000400	Weak transcription	Small Intestine	intestine
4	chr3:51990600-52000400	Weak transcription	HUVEC	blood vessel
5	chr3:51990600-52000800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:51990800-52000400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:51991000-52000200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr3:51991000-52000400	Weak transcription	Stomach Mucosa	stomach
9	chr3:51991000-52000600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:51991200-52000000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr3:51991200-52000400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr3:51991200-52000400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:51991400-52000200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:51992800-52000400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:51993400-52000400	Weak transcription	Osteobl	bone
16	chr3:51994000-52000200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:51994600-52000800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:51995000-52000200	Weak transcription	Esophagus	oesophagus
19	chr3:51995000-52000400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:51995400-52000600	Enhancers	Left Ventricle	heart
21	chr3:51995600-52000400	Enhancers	Right Atrium	heart
22	chr3:51995800-52000200	Enhancers	Fetal Muscle Leg	muscle
23	chr3:51996200-52000200	Enhancers	Right Ventricle	heart
24	chr3:51996200-52001000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:51996400-52000600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:51996600-52001200	Enhancers	Fetal Brain Male	brain
27	chr3:51996600-52001200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr3:51996800-52000400	Enhancers	Fetal Heart	heart
29	chr3:51997200-52000600	Weak transcription	Fetal Intestine Large	intestine
30	chr3:51997600-52000600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:51997800-52001200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:51998000-52000000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr3:51998000-52000200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:51998000-52000800	Enhancers	Pancreas	Pancrea
35	chr3:51998200-52000000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:51998200-52000000	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr3:51998200-52000400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:51998400-52000600	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr3:51998400-52000600	Flanking Active TSS	Brain Substantia Nigra	brain
40	chr3:51998400-52000800	Flanking Active TSS	Brain Cingulate Gyrus	brain
41	chr3:51998400-52000800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr3:51998600-52000200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:51998600-52000400	Enhancers	Colon Smooth Muscle	Colon
44	chr3:51998600-52001200	Flanking Active TSS	Brain Angular Gyrus	brain
45	chr3:51998800-52000400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:51998800-52000600	Enhancers	Gastric	stomach
47	chr3:51998800-52000600	Weak transcription	Ovary	ovary
48	chr3:51999000-52000000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:51999000-52000200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:51999000-52000200	Weak transcription	Fetal Lung	lung

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