Variant report

Variant	rs3813615
Chromosome Location	chr1:161129240-161129241
allele	G/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	TAF1	chr1:161129035-161129564	MCF-7	breast:	n/a	n/a
2	TBL1XR1	chr1:161128973-161129423	GM12878	blood:	n/a	n/a
3	EP300	chr1:161129081-161129352	K562	blood:	n/a	n/a
4	TAF1	chr1:161129021-161129576	SK-N-SH	brain:	n/a	n/a
5	MAX	chr1:161128786-161129649	A549	lung:	n/a	chr1:161129171-161129180 chr1:161129197-161129207 chr1:161129558-161129567
6	POLR2A	chr1:161128767-161130122	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr1:161128526-161129811	GM12892	blood:	n/a	n/a
8	MXI1	chr1:161128966-161129687	HepG2	liver:	n/a	n/a
9	MAX	chr1:161128553-161129981	A549	lung:	n/a	chr1:161129171-161129180 chr1:161129197-161129207 chr1:161129558-161129567
10	NFIC	chr1:161128888-161129430	GM12878	blood:	n/a	n/a
11	REST	chr1:161129096-161129453	PANC-1	pancreas:	n/a	n/a
12	IRF1	chr1:161129018-161129488	K562	blood:	n/a	n/a
13	RUNX3	chr1:161128941-161129519	GM12878	blood:	n/a	n/a
14	TAF1	chr1:161129077-161129697	HepG2	liver:	n/a	n/a
15	MAZ	chr1:161128543-161129837	K562	blood:	n/a	chr1:161129171-161129180 chr1:161129197-161129207 chr1:161129558-161129567
16	SIX5	chr1:161129068-161129397	K562	blood:	n/a	n/a
17	TCF12	chr1:161128485-161129676	A549	lung:	n/a	n/a
18	POLR2A	chr1:161128854-161129916	Raji	blood:	n/a	n/a
19	CREB1	chr1:161129125-161129361	A549	lung:	n/a	n/a
20	MYC	chr1:161128914-161129401	MCF10A-Er-Src	breast:	n/a	chr1:161129171-161129180 chr1:161129197-161129207
21	ZNF384	chr1:161129240-161129263	K562	blood:	n/a	n/a
22	YY1	chr1:161128765-161129906	H1-hESC	embryonic stem cell:	n/a	chr1:161129194-161129208 chr1:161129303-161129323 chr1:161129309-161129321
23	ATF3	chr1:161128877-161129493	A549	lung:	n/a	chr1:161129199-161129208
24	ZBTB33	chr1:161129139-161129375	A549	lung:	n/a	n/a
25	SIN3A	chr1:161129025-161129468	GM12878	blood:	n/a	n/a
26	MTA3	chr1:161128786-161129428	GM12878	blood:	n/a	n/a
27	TEAD4	chr1:161128334-161129348	K562	blood:	n/a	n/a
28	CEBPD	chr1:161128970-161129511	HepG2	liver:	n/a	n/a
29	RCOR1	chr1:161128815-161129349	K562	blood:	n/a	n/a
30	NFIC	chr1:161128895-161129637	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:161128599-161129918	GM12878	blood:	n/a	n/a
32	NRF1	chr1:161128970-161129459	GM12878	blood:	n/a	chr1:161129252-161129263
33	POU2F2	chr1:161128962-161129572	GM12878	blood:	n/a	chr1:161129191-161129203
34	EGR1	chr1:161129034-161129418	GM12878	blood:	n/a	chr1:161129195-161129209 chr1:161129197-161129207 chr1:161129194-161129207
35	ZKSCAN1	chr1:161128925-161129410	Hela-S3	cervix:	n/a	n/a
36	SP4	chr1:161128789-161129489	H1-hESC	embryonic stem cell:	n/a	chr1:161129198-161129209 chr1:161129194-161129210
37	ATF3	chr1:161129038-161129463	A549	lung:	n/a	chr1:161129199-161129208
38	RFX5	chr1:161128933-161129363	HepG2	liver:	n/a	chr1:161129170-161129185 chr1:161129287-161129302 chr1:161129172-161129185 chr1:161129170-161129185
39	POLR2A	chr1:161128921-161129434	GM12892	blood:	n/a	n/a
40	CHD1	chr1:161129196-161129621	GM12878	blood:	n/a	chr1:161129553-161129560
41	IRF1	chr1:161129041-161129432	K562	blood:	n/a	n/a
42	MAX	chr1:161128983-161129444	NB4	blood:	n/a	chr1:161129171-161129180 chr1:161129197-161129207
43	MAX	chr1:161128410-161129925	K562	blood:	n/a	chr1:161129171-161129180 chr1:161129197-161129207 chr1:161129558-161129567
44	POLR2A	chr1:161128814-161130166	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr1:161128826-161129980	H1-neurons	neurons:	n/a	n/a
46	EP300	chr1:161128789-161129626	A549	lung:	n/a	n/a
47	REST	chr1:161128544-161130147	H1-neurons	neurons:	n/a	chr1:161129591-161129604
48	STAT5A	chr1:161128844-161129608	GM12878	blood:	n/a	n/a
49	TAF1	chr1:161129082-161129492	GM12891	blood:	n/a	n/a
50	POLR2A	chr1:161128508-161129847	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:161100691..161104235-chr1:161128857..161130819,4	K562	blood:
2	chr1:161067905..161072134-chr1:161127935..161131211,3	MCF-7	breast:
3	chr1:160231832..160233674-chr1:161127837..161130606,2	MCF-7	breast:
4	chr1:160989787..160992592-chr1:161127591..161130267,2	K562	blood:
5	chr1:161101050..161105947-chr1:161126092..161130683,11	K562	blood:
6	chr1:161128751..161130724-chr1:161170850..161173844,2	MCF-7	breast:
7	chr1:161127959..161129889-chr1:161169079..161171967,3	K562	blood:
8	chr1:161129146..161131988-chr1:161170465..161172275,2	MCF-7	breast:
9	chr1:161085978..161089990-chr1:161127865..161134037,11	K562	blood:
10	chr1:161052998..161054950-chr1:161128036..161130636,2	MCF-7	breast:
11	chr1:160989693..160991522-chr1:161127596..161130418,2	MCF-7	breast:
12	chr1:161101282..161104235-chr1:161127986..161130833,4	MCF-7	breast:
13	chr1:161085658..161090812-chr1:161125926..161133105,17	K562	blood:
14	chr1:161128018..161129911-chr1:161170467..161173789,3	K562	blood:

Variant related genes	Relation type
USP21	TF binding region
ENSG00000224985	TF binding region
ENSG00000132716	Chromatin interaction
ENSG00000228917	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000143256	Chromatin interaction
ENSG00000158864	Chromatin interaction
ENSG00000158796	Chromatin interaction
ENSG00000162755	Chromatin interaction
ENSG00000158793	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12066302	1.00[AFR][1000 genomes]
rs34222337	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161128600-161129400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:161128600-161129600	Active TSS	Primary T cells from cord blood	blood
3	chr1:161128600-161129800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:161128600-161129800	Active TSS	Fetal Brain Female	brain
5	chr1:161128600-161130000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr1:161128600-161130000	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr1:161128600-161130000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:161128600-161130200	Active TSS	H9 Cell Line	embryonic stem cell
9	chr1:161128600-161130800	Transcr. at gene 5' and 3'	Dnd41	blood
10	chr1:161128800-161129600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
11	chr1:161128800-161129800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:161128800-161129800	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
13	chr1:161128800-161129800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:161128800-161129800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr1:161128800-161130000	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr1:161128800-161130000	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr1:161128800-161130000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:161128800-161130000	Active TSS	Psoas Muscle	Psoas
19	chr1:161128800-161130200	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr1:161129000-161129600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:161129000-161129600	Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr1:161129000-161129600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:161129000-161129600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:161129000-161129600	Active TSS	Colonic Mucosa	Colon
25	chr1:161129000-161129600	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr1:161129000-161129600	Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr1:161129000-161129600	Active TSS	Stomach Mucosa	stomach
28	chr1:161129000-161129600	Active TSS	Stomach Smooth Muscle	stomach
29	chr1:161129000-161129600	Active TSS	Thymus	Thymus
30	chr1:161129000-161129800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:161129000-161129800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:161129000-161129800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:161129000-161129800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:161129000-161129800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:161129000-161129800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:161129000-161129800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:161129000-161129800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:161129000-161129800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:161129000-161129800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:161129000-161129800	Active TSS	Aorta	Aorta
41	chr1:161129000-161129800	Active TSS	Brain Anterior Caudate	brain
42	chr1:161129000-161129800	Active TSS	Brain Cingulate Gyrus	brain
43	chr1:161129000-161129800	Active TSS	Brain Germinal Matrix	brain
44	chr1:161129000-161129800	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr1:161129000-161129800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:161129000-161129800	Active TSS	Brain Substantia Nigra	brain
47	chr1:161129000-161129800	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr1:161129000-161129800	Active TSS	Esophagus	oesophagus
49	chr1:161129000-161129800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr1:161129000-161129800	Active TSS	Fetal Heart	heart

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