Variant report

Variant	rs78982507
Chromosome Location	chr3:52000967-52000968
allele	A/C
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	SMARCB1	chr3:52000924-52002227	Hela-S3	cervix:	n/a	n/a
2	ZBTB7A	chr3:52000806-52002473	ECC-1	luminal epithelium:	n/a	chr3:52002005-52002016
3	POLR2A	chr3:52000604-52004386	HepG2	liver:	n/a	n/a
4	MAX	chr3:52000959-52003042	HepG2	liver:	n/a	chr3:52002253-52002263
5	POLR2A	chr3:52000905-52002797	H1-neurons	neurons:	n/a	n/a
6	MXI1	chr3:52000907-52002412	IMR90	lung:	n/a	n/a
7	SMC3	chr3:52000928-52001453	Hela-S3	cervix:	n/a	n/a
8	MAZ	chr3:52000663-52002637	IMR90	lung:	n/a	chr3:52002253-52002263
9	CHD1	chr3:52000913-52001418	IMR90	lung:	n/a	n/a
10	MXI1	chr3:52000959-52001287	GM12878	blood:	n/a	n/a
11	REST	chr3:52000680-52002949	H1-neurons	neurons:	n/a	chr3:52000755-52000768 chr3:52002487-52002500 chr3:52001970-52001983 chr3:52001041-52001061 chr3:52001961-52001979 chr3:52002033-52002046 chr3:52002331-52002344 chr3:52001963-52001976 chr3:52001141-52001154 chr3:52002454-52002467
12	EP300	chr3:52000908-52001505	ECC-1	luminal epithelium:	n/a	chr3:52000976-52000989
13	ELF1	chr3:52000829-52002584	GM12878	blood:	n/a	chr3:52001964-52001976 chr3:52001478-52001490
14	MXI1	chr3:51999719-52003632	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr3:52000308-52002203	K562	blood:	n/a	n/a

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	chr3:51997248..52000056-chr3:52000079..52001783,2	MCF-7	breast:
5	chr3:51976807..51978359-chr3:51999918..52002472,2	K562	blood:
6	chr3:51972287..51978873-chr3:51998179..52003667,9	MCF-7	breast:
7	chr3:51966649..51968588-chr3:51999482..52001370,2	K562	blood:

Variant related genes	Relation type
ABHD14A	TF binding region
PCBP4	TF binding region
ENSG00000114767	Chromatin interaction
ENSG00000090097	Chromatin interaction
ENSG00000041880	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:15 , 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
15	esv3403794	chr3:52000337-52003085	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51996200-52001000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:51996600-52001200	Enhancers	Fetal Brain Male	brain
3	chr3:51996600-52001200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr3:51997800-52001200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:51998600-52001200	Flanking Active TSS	Brain Angular Gyrus	brain
6	chr3:51999000-52001200	Flanking Active TSS	Fetal Brain Female	brain
7	chr3:51999200-52001000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr3:51999200-52001200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:51999200-52001200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:51999600-52001200	Flanking Active TSS	HepG2	liver
11	chr3:51999800-52001000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:51999800-52001200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:51999800-52001200	Flanking Active TSS	HMEC	breast
14	chr3:51999800-52001400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:51999800-52001400	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr3:52000000-52001000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
17	chr3:52000000-52001000	Bivalent Enhancer	Fetal Thymus	thymus
18	chr3:52000000-52001000	Enhancers	Spleen	Spleen
19	chr3:52000000-52001200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:52000000-52001200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:52000000-52001200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr3:52000000-52001200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:52000000-52001200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
24	chr3:52000000-52001200	Flanking Active TSS	HSMM	muscle
25	chr3:52000200-52001200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:52000200-52001200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:52000200-52001200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
28	chr3:52000200-52001200	Flanking Active TSS	Fetal Muscle Leg	muscle
29	chr3:52000200-52001200	Flanking Active TSS	Right Ventricle	heart
30	chr3:52000200-52001400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:52000200-52002000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:52000200-52002200	Active TSS	HSMMtube	muscle
33	chr3:52000400-52001000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:52000400-52001000	Enhancers	Liver	Liver
35	chr3:52000400-52001000	Enhancers	Small Intestine	intestine
36	chr3:52000400-52001200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:52000400-52001200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:52000400-52001200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr3:52000400-52001200	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr3:52000400-52001200	Flanking Active TSS	Fetal Heart	heart
41	chr3:52000400-52001200	Flanking Active TSS	Fetal Stomach	stomach
42	chr3:52000400-52001200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
43	chr3:52000400-52001200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr3:52000400-52001200	Flanking Active TSS	HUVEC	blood vessel
45	chr3:52000400-52001400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:52000400-52001400	Flanking Active TSS	Dnd41	blood
47	chr3:52000400-52002000	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr3:52000400-52002600	Active TSS	Fetal Kidney	kidney
49	chr3:52000400-52002600	Active TSS	Rectal Smooth Muscle	rectum
50	chr3:52000600-52001000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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