Variant report

Variant	rs576616742
Chromosome Location	chr3:142839443-142839444
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	UBTF	chr3:142837331-142839986	K562	blood:	n/a	n/a
2	ZNF263	chr3:142837735-142839609	HEK293-T-REx	kidney:	n/a	chr3:142839428-142839437
3	POLR2A	chr3:142837773-142841232	GM19193	blood:	n/a	n/a
4	POLR2A	chr3:142837235-142842973	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:142837371-142841744	GM12892	blood:	n/a	n/a
6	POLR2A	chr3:142839092-142839552	GM12891	blood:	n/a	n/a
7	POLR2A	chr3:142837327-142842927	GM12891	blood:	n/a	n/a
8	POLR2A	chr3:142836914-142843085	GM12891	blood:	n/a	n/a
9	POLR2A	chr3:142837796-142841213	GM12878	blood:	n/a	n/a
10	PML	chr3:142837665-142840120	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:142839160-142839468	K562	blood:	n/a	n/a
12	POLR2A	chr3:142837397-142840013	GM12892	blood:	n/a	n/a
13	POLR2A	chr3:142839436-142839747	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr3:142837372-142842950	GM12891	blood:	n/a	n/a
15	ZBTB7A	chr3:142837837-142839574	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr3:142837824-142840822	GM12878	blood:	n/a	n/a
17	E2F6	chr3:142838899-142840803	H1-hESC	embryonic stem cell:	n/a	chr3:142838914-142838924 chr3:142838911-142838921 chr3:142839536-142839546 chr3:142839574-142839584 chr3:142839630-142839639 chr3:142839543-142839552 chr3:142838917-142838927
18	CHD1	chr3:142838568-142839462	GM12878	blood:	n/a	n/a
19	EBF1	chr3:142839209-142839620	GM12878	blood:	n/a	n/a
20	SIN3A	chr3:142837580-142840494	H1-hESC	embryonic stem cell:	n/a	chr3:142839059-142839070 chr3:142839574-142839587 chr3:142839203-142839214 chr3:142838852-142838863 chr3:142839021-142839030
21	MAX	chr3:142838103-142839488	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr3:142837371-142840452	GM12892	blood:	n/a	n/a
23	RAD21	chr3:142839030-142839470	H1-hESC	embryonic stem cell:	n/a	chr3:142839044-142839054
24	HEY1	chr3:142839081-142839506	K562	blood:	n/a	chr3:142839206-142839221
25	MAX	chr3:142839135-142840430	K562	blood:	n/a	n/a
26	POLR2A	chr3:142839356-142839482	MCF10A-Er-Src	breast:	n/a	n/a
27	SIN3AK20	chr3:142838978-142839520	H1-hESC	embryonic stem cell:	n/a	n/a
28	HMGN3	chr3:142837835-142840246	K562	blood:	n/a	n/a
29	SPI1	chr3:142839229-142839515	GM12891	blood:	n/a	chr3:142839429-142839442
30	YY1	chr3:142839038-142840483	GM12892	blood:	n/a	chr3:142839630-142839639 chr3:142839364-142839378 chr3:142839628-142839642
31	RUNX3	chr3:142837697-142840604	GM12878	blood:	n/a	n/a
32	MTA3	chr3:142837353-142839597	GM12878	blood:	n/a	n/a
33	PAX5	chr3:142838058-142840101	GM12892	blood:	n/a	n/a
34	CTCF	chr3:142839420-142839570	GM12871	blood:	n/a	n/a
35	RAD21	chr3:142839092-142839529	H1-hESC	embryonic stem cell:	n/a	n/a
36	UBTF	chr3:142837118-142840212	K562	blood:	n/a	n/a
37	POLR2A	chr3:142837700-142841323	K562	blood:	n/a	n/a
38	CTCF	chr3:142839228-142839460	GM12892	blood:	n/a	n/a
39	CTCF	chr3:142839360-142839510	GM12864	blood:	n/a	n/a
40	ZBTB7A	chr3:142837837-142839530	ECC-1	luminal epithelium:	n/a	n/a
41	ZNF143	chr3:142838980-142840529	GM12878	blood:	n/a	chr3:142839542-142839552
42	POLR2A	chr3:142837654-142842994	GM12892	blood:	n/a	n/a
43	GABPA	chr3:142839021-142839531	K562	blood:	n/a	n/a
44	POLR2A	chr3:142837616-142840005	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr3:142837455-142842924	GM18505	blood:	n/a	n/a
46	POLR2A	chr3:142837752-142841154	GM15510	blood:	n/a	n/a
47	POLR2A	chr3:142839238-142839597	K562	blood:	n/a	n/a
48	CCNT2	chr3:142837807-142840892	K562	blood:	n/a	chr3:142837856-142837865
49	ZBTB7A	chr3:142837791-142839816	K562	blood:	n/a	n/a
50	GABPA	chr3:142838988-142839737	H1-hESC	embryonic stem cell:	n/a	chr3:142839543-142839552

No.	Distal block	Cell Line	Cell type
1	chr3:142777135..142778996-chr3:142838578..142841035,2	K562	blood:
2	chr3:142795942..142798929-chr3:142838470..142841083,3	K562	blood:
3	chr3:142839097..142841882-chr3:143060810..143062990,2	K562	blood:
4	chr3:142760861..142763721-chr3:142838517..142840129,2	K562	blood:
5	chr3:142546469..142548561-chr3:142838535..142840408,2	K562	blood:
6	chr3:142719801..142721977-chr3:142838395..142840175,2	K562	blood:
7	chr3:142772025..142774338-chr3:142838383..142839930,2	K562	blood:
8	chr3:142729466..142732055-chr3:142838748..142841571,2	K562	blood:
9	chr3:142755305..142760138-chr3:142835756..142840820,6	K562	blood:
10	chr3:142839303..142841374-chr3:143036089..143037614,2	K562	blood:
11	chr3:142838518..142840970-chr3:143064617..143066302,2	K562	blood:

Variant related genes	Relation type
ENSG00000241679	TF binding region
ENSG00000240012	Chromatin interaction
ENSG00000268129	Chromatin interaction
ENSG00000240950	Chromatin interaction
ENSG00000163714	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv591921	chr3:142762487-142841740	Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1007164	chr3:142837004-142891719	Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv3438597	chr3:142838687-142841235	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a
8	esv3421903	chr3:142839312-142842010	Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142837000-142840400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr3:142837200-142840600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
3	chr3:142837400-142839800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
4	chr3:142837400-142840200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:142837400-142840400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:142837400-142840400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:142837400-142840600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr3:142837600-142839600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:142837600-142839800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:142837600-142840200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:142837600-142840200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:142837600-142840200	Active TSS	Right Atrium	heart
13	chr3:142837600-142840200	Active TSS	K562	blood
14	chr3:142837600-142840400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:142837600-142840400	Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr3:142837600-142840400	Active TSS	Brain Hippocampus Middle	brain
17	chr3:142837600-142840400	Active TSS	Brain Substantia Nigra	brain
18	chr3:142837600-142840400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr3:142837600-142840400	Active TSS	HSMMtube	muscle
20	chr3:142837600-142840400	Active TSS	NHDF-Ad	bronchial
21	chr3:142837600-142840600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:142837600-142840600	Active TSS	Primary T cells from cord blood	blood
23	chr3:142837600-142840600	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr3:142837600-142840600	Active TSS	NHLF	lung
25	chr3:142837600-142840600	Active TSS	Osteobl	bone
26	chr3:142837600-142840800	Active TSS	Brain Anterior Caudate	brain
27	chr3:142837600-142840800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:142837600-142841000	Active TSS	HSMM	muscle
29	chr3:142837600-142841200	Active TSS	Brain Angular Gyrus	brain
30	chr3:142837800-142839600	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr3:142837800-142839600	Active TSS	Rectal Smooth Muscle	rectum
32	chr3:142837800-142839600	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr3:142837800-142839800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:142837800-142839800	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr3:142837800-142839800	Active TSS	NH-A	brain
36	chr3:142837800-142840000	Active TSS	Muscle Satellite Cultured Cells	--
37	chr3:142837800-142840000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:142837800-142840000	Bivalent/Poised TSS	Fetal Brain Female	brain
39	chr3:142837800-142840200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:142837800-142840200	Active TSS	Ovary	ovary
41	chr3:142837800-142840200	Active TSS	Small Intestine	intestine
42	chr3:142837800-142840200	Active TSS	Spleen	Spleen
43	chr3:142837800-142840400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:142837800-142840400	Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr3:142837800-142840400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
46	chr3:142837800-142840600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:142837800-142840600	Active TSS	Brain Cingulate Gyrus	brain
48	chr3:142837800-142843400	Active TSS	Fetal Kidney	kidney
49	chr3:142838000-142839600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:142838000-142839600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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