Variant report

Variant	rs555734608
Chromosome Location	chr4:129731392-129731393
allele	A/G
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	chr4:129730542-129731475	HL-60	blood:	n/a	n/a
2	CHD1	chr4:129730550-129733472	H1-hESC	embryonic stem cell:	n/a	chr4:129732389-129732399 chr4:129733422-129733432 chr4:129733260-129733270 chr4:129733062-129733072
3	MXI1	chr4:129730257-129734736	IMR90	lung:	n/a	n/a
4	POLR2A	chr4:129730532-129734022	HCT-116	colon:	n/a	n/a
5	HEY1	chr4:129730588-129731480	K562	blood:	n/a	chr4:129730719-129730734
6	POLR2A	chr4:129730570-129731542	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr4:129730561-129734095	K562	blood:	n/a	n/a
8	JUND	chr4:129731161-129731396	HepG2	liver:	n/a	n/a
9	RUNX3	chr4:129731075-129733957	GM12878	blood:	n/a	n/a
10	TAF1	chr4:129730594-129731431	K562	blood:	n/a	n/a
11	RCOR1	chr4:129731279-129733593	GM12878	blood:	n/a	n/a
12	POLR2A	chr4:129730506-129734115	K562	blood:	n/a	n/a
13	PBX3	chr4:129730581-129731515	SK-N-SH	brain:	n/a	n/a
14	REST	chr4:129730404-129731586	H1-neurons	neurons:	n/a	chr4:129730675-129730688
15	POLR2A	chr4:129730508-129731416	U87	brain:	n/a	n/a
16	POLR2A	chr4:129731261-129734094	K562	blood:	n/a	n/a
17	TAF1	chr4:129730568-129731511	SK-N-SH	brain:	n/a	n/a
18	ZBTB7A	chr4:129730462-129731678	ECC-1	luminal epithelium:	n/a	chr4:129731474-129731488
19	POLR2A	chr4:129730599-129734478	GM18505	blood:	n/a	n/a
20	WRNIP1	chr4:129731252-129731426	GM12878	blood:	n/a	n/a
21	CREB1	chr4:129730516-129731599	H1-hESC	embryonic stem cell:	n/a	n/a
22	RELA	chr4:129730601-129734033	GM12891	blood:	n/a	n/a
23	POLR2A	chr4:129730637-129734008	GM12878	blood:	n/a	n/a
24	ATF2	chr4:129731142-129731783	GM12878	blood:	n/a	n/a
25	ZMIZ1	chr4:129731273-129731432	K562	blood:	n/a	n/a
26	UBTF	chr4:129730658-129731441	K562	blood:	n/a	n/a
27	POLR2A	chr4:129730510-129734063	Raji	blood:	n/a	n/a
28	MYC	chr4:129730573-129733589	Hela-S3	cervix:	n/a	chr4:129732622-129732632 chr4:129732621-129732632 chr4:129732618-129732633 chr4:129732623-129732630 chr4:129732622-129732631 chr4:129732396-129732406 chr4:129733335-129733345 chr4:129733276-129733286
29	POLR2A	chr4:129730519-129731751	PBDE	blood:	n/a	n/a
30	RCOR1	chr4:129730574-129731509	K562	blood:	n/a	n/a
31	RAD21	chr4:129730551-129731406	SK-N-SH_RA	brain:	n/a	chr4:129730800-129730814 chr4:129730771-129730780
32	POLR2A	chr4:129730623-129734071	GM12891	blood:	n/a	n/a
33	POLR2A	chr4:129730570-129731420	GM12878	blood:	n/a	n/a
34	TCF12	chr4:129730492-129734183	A549	lung:	n/a	chr4:129733244-129733251
35	YY1	chr4:129730550-129731481	H1-hESC	embryonic stem cell:	n/a	chr4:129731377-129731391
36	POLR2A	chr4:129730588-129731470	HepG2	liver:	n/a	n/a
37	POLR2A	chr4:129730608-129731436	GM12878	blood:	n/a	n/a
38	MAX	chr4:129730407-129734144	A549	lung:	n/a	chr4:129732622-129732632 chr4:129732621-129732632 chr4:129732618-129732633 chr4:129732623-129732630 chr4:129732622-129732631 chr4:129732396-129732406 chr4:129733335-129733345 chr4:129733276-129733286
39	POLR2A	chr4:129730629-129733969	NB4	blood:	n/a	n/a
40	TBL1XR1	chr4:129731277-129731509	K562	blood:	n/a	n/a
41	NFIC	chr4:129731155-129732732	GM12878	blood:	n/a	n/a
42	POLR2A	chr4:129730691-129734532	HepG2	liver:	n/a	n/a
43	MYC	chr4:129731219-129731557	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr4:129730654-129731449	MCF-7	breast:	n/a	n/a
45	YY1	chr4:129731055-129731515	A549	lung:	n/a	chr4:129731377-129731391
46	CREB1	chr4:129730514-129732046	K562	blood:	n/a	n/a
47	RAD21	chr4:129730297-129732679	SK-N-SH	brain:	n/a	chr4:129730800-129730814 chr4:129730771-129730780
48	POLR2A	chr4:129730677-129734001	HEK293	kidney:	n/a	n/a
49	ATF2	chr4:129731119-129731494	GM12878	blood:	n/a	n/a
50	ZNF263	chr4:129730500-129731454	HEK293-T-REx	kidney:	n/a	chr4:129731393-129731402

No.	Distal block	Cell Line	Cell type
1	chr1:228352349..228353216-chr4:129731096..129731690,2	Hela-S3	cervix:
2	chr4:129375160..129378617-chr4:129730147..129733611,3	MCF-7	breast:
3	chr4:128980795..128984031-chr4:129730059..129735028,7	K562	blood:
4	chr4:129471355..129474956-chr4:129730853..129734024,4	MCF-7	breast:
5	chr4:129208294..129210116-chr4:129731375..129734707,3	MCF-7	breast:
6	chr4:129374782..129377512-chr4:129729521..129732215,3	K562	blood:
7	chr11:62608655..62609419-chr4:129731014..129731869,3	Hela-S3	cervix:
8	chr4:129391462..129394361-chr4:129730843..129732581,2	K562	blood:
9	chr4:128980795..128982891-chr4:129730267..129732892,3	K562	blood:
10	chr4:129521846..129523851-chr4:129730837..129734105,3	K562	blood:
11	chr4:129730688..129731418-chr6:24720530..24721134,2	Hela-S3	cervix:
12	chr16:402353..402985-chr4:129731353..129732296,2	Hela-S3	cervix:
13	chr4:129488526..129491708-chr4:129730813..129734421,3	K562	blood:
14	chr4:129491375..129494260-chr4:129730648..129733095,2	MCF-7	breast:
15	chr4:129206178..129209498-chr4:129731212..129733921,5	K562	blood:
16	chr4:129518963..129527383-chr4:129727996..129735335,14	K562	blood:
17	chr4:129206178..129209105-chr4:129728853..129732712,4	K562	blood:
18	chr4:129731326..129732115-chr6:26158771..26159658,2	Hela-S3	cervix:
19	chr4:129473168..129475213-chr4:129730479..129732295,2	K562	blood:
20	chr4:129209335..129213237-chr4:129730288..129733311,3	K562	blood:
21	chr4:129730547..129732304-chr4:129732580..129735331,2	MCF-7	breast:
22	chr4:129376012..129378140-chr4:129729596..129731686,2	K562	blood:
23	chr4:129731357..129734214-chr4:129752200..129753715,2	K562	blood:
24	chr4:129472659..129478043-chr4:129729703..129733779,4	K562	blood:
25	chr4:129730340..129733748-chr4:130013373..130016609,5	K562	blood:

Variant related genes	Relation type
JADE1	TF binding region
ENSG00000112308	Chromatin interaction
ENSG00000273077	Chromatin interaction
ENSG00000138709	Chromatin interaction
ENSG00000103126	Chromatin interaction
ENSG00000251432	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000248187	Chromatin interaction
ENSG00000164040	Chromatin interaction
ENSG00000151470	Chromatin interaction
ENSG00000151466	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000248802	Chromatin interaction
ENSG00000077684	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1020801	chr4:129658178-129778086	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv537248	chr4:129658178-129778086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv822717	chr4:129724785-129739862	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	n/a
5	esv3340336	chr4:129730252-129734500	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129730000-129734000	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr4:129730200-129734200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:129730200-129734200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr4:129730200-129734200	Active TSS	K562	blood
5	chr4:129730200-129734400	Active TSS	NHDF-Ad	bronchial
6	chr4:129730400-129731400	Active TSS	Primary hematopoietic stem cells	blood
7	chr4:129730400-129731400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:129730400-129732000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:129730400-129732000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:129730400-129732000	Active TSS	Placenta	Placenta
11	chr4:129730400-129732000	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr4:129730400-129732000	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr4:129730400-129732200	Active TSS	Right Atrium	heart
14	chr4:129730400-129733600	Active TSS	Primary T cells fromperipheralblood	blood
15	chr4:129730400-129733600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:129730400-129733600	Active TSS	Thymus	Thymus
17	chr4:129730400-129733800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:129730400-129733800	Active TSS	Primary T cells from cord blood	blood
19	chr4:129730400-129733800	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr4:129730400-129733800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:129730400-129733800	Active TSS	Brain Cingulate Gyrus	brain
22	chr4:129730400-129733800	Active TSS	Brain Hippocampus Middle	brain
23	chr4:129730400-129733800	Active TSS	Fetal Brain Female	brain
24	chr4:129730400-129733800	Active TSS	Fetal Kidney	kidney
25	chr4:129730400-129733800	Active TSS	Fetal Muscle Leg	muscle
26	chr4:129730400-129733800	Active TSS	Fetal Thymus	thymus
27	chr4:129730400-129733800	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr4:129730400-129733800	Active TSS	Stomach Smooth Muscle	stomach
29	chr4:129730400-129733800	Active TSS	Osteobl	bone
30	chr4:129730400-129734000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:129730400-129734000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:129730400-129734000	Active TSS	Fetal Intestine Large	intestine
33	chr4:129730400-129734000	Active TSS	Pancreas	Pancrea
34	chr4:129730400-129734000	Active TSS	Rectal Smooth Muscle	rectum
35	chr4:129730400-129734000	Active TSS	NHEK	skin
36	chr4:129730400-129734200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr4:129730400-129734200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:129730400-129734200	Active TSS	Brain Angular Gyrus	brain
39	chr4:129730400-129734200	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr4:129730400-129734200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr4:129730400-129734200	Active TSS	Brain Substantia Nigra	brain
42	chr4:129730400-129734200	Active TSS	Colon Smooth Muscle	Colon
43	chr4:129730400-129734200	Active TSS	Fetal Muscle Trunk	muscle
44	chr4:129730400-129734200	Active TSS	Left Ventricle	heart
45	chr4:129730400-129734200	Active TSS	Ovary	ovary
46	chr4:129730400-129734200	Active TSS	HSMM	muscle
47	chr4:129730400-129734200	Active TSS	HSMMtube	muscle
48	chr4:129730400-129734400	Active TSS	Brain Anterior Caudate	brain
49	chr4:129730400-129734400	Active TSS	Psoas Muscle	Psoas
50	chr4:129730400-129734400	Active TSS	GM12878-XiMat	blood

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