Variant report

Variant	rs6768628
Chromosome Location	chr3:156269368-156269369
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	TEAD4	chr3:156268914-156270090	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr3:156269140-156269962	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:156268971-156270753	HUVEC	blood vessel:	n/a	n/a
4	NFIC	chr3:156268930-156270124	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr3:156268961-156270023	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr3:156268965-156269402	HUVEC	blood vessel:	n/a	n/a
7	FOS	chr3:156269111-156269867	HUVEC	blood vessel:	n/a	chr3:156269680-156269691
8	GATA2	chr3:156269148-156269514	SH-SY5Y	brain:	n/a	chr3:156269313-156269327 chr3:156269323-156269332
9	EP300	chr3:156268816-156269991	SK-N-SH	brain:	n/a	n/a
10	GATA2	chr3:156269161-156269790	HUVEC	blood vessel:	n/a	chr3:156269313-156269327 chr3:156269323-156269332
11	POLR2A	chr3:156269138-156269487	GM12878	blood:	n/a	n/a
12	JUND	chr3:156268918-156270089	SK-N-SH	brain:	n/a	n/a
13	TEAD4	chr3:156269046-156269952	SK-N-SH	brain:	n/a	n/a
14	GATA3	chr3:156268852-156270070	SK-N-SH	brain:	n/a	chr3:156269323-156269332
15	FOSL2	chr3:156268924-156269983	SK-N-SH	brain:	n/a	n/a
16	JUND	chr3:156268836-156270039	SK-N-SH	brain:	n/a	n/a
17	GATA3	chr3:156269229-156269465	SH-SY5Y	brain:	n/a	chr3:156269323-156269332
18	POLR2A	chr3:156267070-156269885	K562	blood:	n/a	n/a
19	POLR2A	chr3:156269143-156269415	Hela-S3	cervix:	n/a	n/a
20	TCF12	chr3:156268804-156270217	SK-N-SH	brain:	n/a	chr3:156269754-156269762
21	GATA3	chr3:156268775-156270071	SK-N-SH	brain:	n/a	chr3:156269323-156269332
22	POLR2A	chr3:156268564-156270659	HepG2	liver:	n/a	n/a
23	POLR2A	chr3:156269187-156269785	GM12878	blood:	n/a	n/a
24	MEF2A	chr3:156268941-156270036	SK-N-SH	brain:	n/a	chr3:156269451-156269465 chr3:156269446-156269467 chr3:156269446-156269467 chr3:156269446-156269467 chr3:156269790-156269801 chr3:156269451-156269466
25	PBX3	chr3:156268874-156270093	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr3:156269082-156269508	K562	blood:	n/a	n/a
27	YY1	chr3:156268928-156269969	SK-N-SH	brain:	n/a	chr3:156269432-156269448 chr3:156269436-156269444 chr3:156269023-156269033
28	FOSL2	chr3:156268820-156269991	SK-N-SH	brain:	n/a	n/a
29	EP300	chr3:156268839-156270076	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr3:156269150-156269412	K562	blood:	n/a	n/a
31	PBX3	chr3:156268961-156269990	SK-N-SH	brain:	n/a	n/a
32	MAX	chr3:156268971-156269431	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr3:156269152-156269966	IMR90	lung:	n/a	n/a
34	POLR2A	chr3:156269128-156269495	HepG2	liver:	n/a	n/a
35	TCF12	chr3:156268808-156270097	SK-N-SH	brain:	n/a	chr3:156269754-156269762
36	MAFK	chr3:156269165-156269824	IMR90	lung:	n/a	chr3:156269680-156269690
37	WRNIP1	chr3:156269191-156269392	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:156268357..156274553-chr3:156389283..156394606,15	MCF-7	breast:
2	chr3:156260735..156275674-chr3:156389736..156397850,44	K562	blood:
3	chr3:156267109..156271448-chr3:156870440..156873447,4	K562	blood:
4	chr3:156267016..156271448-chr3:156870182..156873447,4	K562	blood:
5	chr3:156268894..156273100-chr3:156541711..156545313,4	MCF-7	breast:
6	chr3:156264459..156269953-chr3:156392362..156396309,4	K562	blood:

Variant related genes	Relation type
SSR3	TF binding region
ENSG00000197980	Chromatin interaction
ENSG00000163660	Chromatin interaction
ENSG00000201778	Chromatin interaction
ENSG00000243926	Chromatin interaction
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10513493	0.83[AFR][1000 genomes]
rs7631469	1.00[AMR][1000 genomes]
rs7631824	1.00[AMR][1000 genomes]
rs7631828	1.00[AMR][1000 genomes]
rs7643608	1.00[AMR][1000 genomes]
rs7653891	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv829764	chr3:156174824-156347774	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
3	nsv877683	chr3:156180366-156272351	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 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	chr3:156252000-156270200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr3:156253600-156271400	Weak transcription	Stomach Mucosa	stomach
3	chr3:156253800-156270800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr3:156254200-156270200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr3:156255200-156270600	Strong transcription	A549	lung
6	chr3:156255600-156270800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:156255800-156270200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:156255800-156270200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:156255800-156270600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr3:156255800-156270800	Strong transcription	Fetal Intestine Large	intestine
11	chr3:156256200-156270400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:156256200-156270400	Strong transcription	Primary hematopoietic stem cells	blood
13	chr3:156256400-156270400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:156256600-156270600	Strong transcription	Primary B cells from cord blood	blood
15	chr3:156256800-156269400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:156256800-156269600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:156256800-156270600	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:156256800-156271000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:156257000-156269600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:156257000-156270400	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr3:156257000-156270600	Strong transcription	Fetal Thymus	thymus
22	chr3:156257000-156271000	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr3:156257000-156271200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr3:156257200-156269600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:156257200-156270200	Strong transcription	Hela-S3	cervix
26	chr3:156257800-156270200	Weak transcription	Aorta	Aorta
27	chr3:156257800-156270600	Weak transcription	Fetal Brain Male	brain
28	chr3:156258400-156270400	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr3:156258800-156270400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:156258800-156270600	Strong transcription	Primary B cells from peripheral blood	blood
31	chr3:156259200-156270800	Strong transcription	Placenta	Placenta
32	chr3:156259400-156271000	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr3:156259800-156271200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:156261200-156271200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:156261600-156269600	Weak transcription	Esophagus	oesophagus
36	chr3:156262000-156271800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr3:156263000-156270400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:156263200-156270800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:156265000-156270800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
40	chr3:156265600-156269400	Genic enhancers	NHDF-Ad	bronchial
41	chr3:156265600-156270000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:156265600-156270800	Genic enhancers	Adipose Nuclei	Adipose
43	chr3:156266000-156271000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
44	chr3:156266000-156271600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr3:156266400-156269400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr3:156266400-156269400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:156266400-156270200	Genic enhancers	HepG2	liver
48	chr3:156266400-156270400	Weak transcription	Brain Germinal Matrix	brain
49	chr3:156266400-156271400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:156266400-156271400	Weak transcription	Colonic Mucosa	Colon

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