Variant report

Variant	rs11963039
Chromosome Location	chr6:147525655-147525656
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:145)
CpG islands
(count:61)
Chromatin interactive
region (count:9)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:145 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr6:147523374-147526232	H1-neurons	neurons:	n/a	chr6:147525376-147525389
2	TAF1	chr6:147525357-147525885	H1-hESC	embryonic stem cell:	n/a	n/a
3	SPI1	chr6:147525337-147525918	HL-60	blood:	n/a	n/a
4	ELF1	chr6:147525263-147525857	K562	blood:	n/a	chr6:147525386-147525398 chr6:147525391-147525400 chr6:147525388-147525397 chr6:147525385-147525394 chr6:147525389-147525401
5	MAZ	chr6:147523081-147526390	K562	blood:	n/a	n/a
6	POLR2A	chr6:147525555-147526416	K562	blood:	n/a	n/a
7	POLR2A	chr6:147523534-147526020	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr6:147525460-147525750	GM12874	blood:	n/a	n/a
9	POLR2A	chr6:147522937-147526034	K562	blood:	n/a	n/a
10	HCFC1	chr6:147523021-147525697	K562	blood:	n/a	n/a
11	MAX	chr6:147523514-147525872	K562	blood:	n/a	n/a
12	SIN3AK20	chr6:147523469-147525845	PANC-1	pancreas:	n/a	n/a
13	RCOR1	chr6:147525587-147526430	K562	blood:	n/a	n/a
14	TAF1	chr6:147525278-147525929	K562	blood:	n/a	n/a
15	POLR2A	chr6:147523562-147525855	Gliobla	brain:	n/a	n/a
16	POLR2A	chr6:147524706-147525859	GM12878	blood:	n/a	n/a
17	UBTF	chr6:147523633-147526451	K562	blood:	n/a	n/a
18	MAX	chr6:147525460-147525946	ECC-1	luminal epithelium:	n/a	n/a
19	TBP	chr6:147524608-147525868	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZBTB7A	chr6:147525530-147525710	HepG2	liver:	n/a	n/a
21	POLR2A	chr6:147525629-147525771	A549	lung:	n/a	n/a
22	POLR2A	chr6:147523072-147526476	Hela-S3	cervix:	n/a	n/a
23	RAD21	chr6:147523131-147526026	IMR90	lung:	n/a	n/a
24	EP300	chr6:147525476-147525683	K562	blood:	n/a	chr6:147525502-147525511 chr6:147525476-147525485
25	MXI1	chr6:147523062-147525873	IMR90	lung:	n/a	chr6:147523964-147523973
26	ZBTB7A	chr6:147525386-147525900	ECC-1	luminal epithelium:	n/a	chr6:147525868-147525882
27	POLR2A	chr6:147523101-147525939	GM18505	blood:	n/a	n/a
28	POLR2A	chr6:147523500-147526423	K562	blood:	n/a	n/a
29	POLR2A	chr6:147523491-147526020	H1-neurons	neurons:	n/a	n/a
30	TAF1	chr6:147525236-147525902	H1-neurons	neurons:	n/a	n/a
31	POLR2A	chr6:147522918-147526334	GM12891	blood:	n/a	n/a
32	TAF1	chr6:147525607-147525898	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr6:147522937-147525994	HL-60	blood:	n/a	n/a
34	FOXM1	chr6:147525293-147525956	GM12878	blood:	n/a	n/a
35	SMARCB1	chr6:147523679-147525971	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr6:147525552-147525887	H1-hESC	embryonic stem cell:	n/a	n/a
37	ETS1	chr6:147524712-147525996	K562	blood:	n/a	chr6:147525389-147525400 chr6:147525386-147525397 chr6:147524778-147524791 chr6:147525496-147525510 chr6:147525383-147525394
38	POLR2A	chr6:147523069-147525928	GM19099	blood:	n/a	n/a
39	POLR2A	chr6:147523076-147525951	GM19193	blood:	n/a	n/a
40	RAD21	chr6:147525444-147525924	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr6:147524731-147525867	GM12878	blood:	n/a	n/a
42	ZBTB7A	chr6:147525337-147525834	K562	blood:	n/a	n/a
43	POLR2A	chr6:147523023-147525871	K562	blood:	n/a	n/a
44	MAX	chr6:147525311-147525877	NB4	blood:	n/a	n/a
45	SIN3AK20	chr6:147525447-147525829	PFSK-1	brain:	n/a	n/a
46	POLR2A	chr6:147523019-147525931	Raji	blood:	n/a	n/a
47	ZBTB7A	chr6:147525393-147525873	K562	blood:	n/a	n/a
48	YY1	chr6:147525465-147525758	GM12878	blood:	n/a	n/a
49	POLR2A	chr6:147522948-147526030	GM12878	blood:	n/a	n/a
50	POLR2A	chr6:147522948-147525994	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:147525648-147525698	AG09309	skin:	n/a
2	chr6:147525648-147525698	NHDF-neo	bronchial:	n/a
3	chr6:147525648-147525698	Caco-2	colon:	n/a
4	chr6:147525648-147525698	HRCEpiC	kidney:	n/a
5	chr6:147525648-147525698	H1-hESC	embryonic stem cell:	embryo
6	chr6:147525648-147525698	HCM	heart:	n/a
7	chr6:147525648-147525698	HRE	kidney:	n/a
8	chr6:147525648-147525698	T-47D	breast:	n/a
9	chr6:147525648-147525698	HEEpiC	esophagus:	n/a
10	chr6:147525648-147525698	BJ	skin:	n/a
11	chr6:147525648-147525698	CMK	blood:	n/a
12	chr6:147525648-147525698	HAEpiC	amniotic membrane:	n/a
13	chr6:147525648-147525698	SAEC	small airway:	n/a
14	chr6:147525648-147525698	AoSMC	blood vessel:	n/a
15	chr6:147525648-147525698	HL-60	blood:	n/a
16	chr6:147525648-147525698	HRPEpiC	eye:	n/a
17	chr6:147525648-147525698	Hepatocyte	liver:	n/a
18	chr6:147525648-147525698	PANC-1	pancreas:	n/a
19	chr6:147525648-147525698	LNCaP	prostate:	n/a
20	chr6:147525648-147525698	BE2_C	brain:	n/a
21	chr6:147525648-147525698	SK-N-SH_RA	brain:	n/a
22	chr6:147525648-147525698	HIPEpiC	eye:	n/a
23	chr6:147525648-147525698	NHBE	bronchial:	n/a
24	chr6:147525648-147525698	HCPEpiC	choroid plexus:	n/a
25	chr6:147525648-147525698	HCT-116	colon:	n/a
26	chr6:147525648-147525698	MCF10A-Er-Src	breast:	n/a
27	chr6:147525648-147525698	HepG2	liver:	n/a
28	chr6:147525648-147525698	U87	brain:	n/a
29	chr6:147525648-147525698	HPAEpiC	pulmonary alveolar:	n/a
30	chr6:147525648-147525698	HCF	heart:	n/a
31	chr6:147525648-147525698	NB4	blood:	n/a
32	chr6:147525648-147525698	HNPCEpiC	eye:	n/a
33	chr6:147525648-147525698	SK-N-MC	brain:	n/a
34	chr6:147525648-147525698	GM19239	blood:	n/a
35	chr6:147525648-147525698	SKMC	muscle:	n/a
36	chr6:147525648-147525698	HMEC	breast:	n/a
37	chr6:147525648-147525698	NH-A	brain:	n/a
38	chr6:147525648-147525698	ovcar-3	ovarian:	n/a
39	chr6:147525648-147525698	MCF-7	breast:	n/a
40	chr6:147525648-147525698	NT2-D1	testis:	n/a
41	chr6:147525648-147525698	SK-N-SH	brain:	n/a
42	chr6:147525648-147525698	Hela-S3	cervix:	n/a
43	chr6:147525648-147525698	AG10803	skin:	n/a
44	chr6:147525648-147525698	PFSK-1	brain:	n/a
45	chr6:147525648-147525698	ECC-1	luminal epithelium:	n/a
46	chr6:147525648-147525698	HEK293	kidney:	embryo
47	chr6:147525648-147525698	K562	blood:	n/a
48	chr6:147525648-147525698	AG09319	gingival:	n/a
49	chr6:147525648-147525698	GM06990	blood:	n/a
50	chr6:147525648-147525698	AG04449	skin:	fetal

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:147229677..147239083-chr6:147521152..147530893,22	K562	blood:
2	chr6:147475725..147486468-chr6:147521132..147528058,22	K562	blood:
3	chr6:135817566..135820390-chr6:147524276..147525845,2	K562	blood:
4	chr6:147477631..147490692-chr6:147521132..147530003,24	K562	blood:
5	chr6:147478214..147481987-chr6:147524471..147526667,3	MCF-7	breast:
6	chr6:147178857..147181755-chr6:147524235..147526085,2	MCF-7	breast:
7	chr6:147232346..147237544-chr6:147521050..147527983,13	K562	blood:
8	chr6:147231935..147237791-chr6:147522176..147527834,11	MCF-7	breast:
9	chr6:147233166..147237387-chr6:147522685..147525854,6	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SHPRH-2	chr6:147525549-147525676	ENSG00000233452
2	lnc-SHPRH-2	chr6:147525549-147525750	NONHSAT115433

No data

Variant related genes	Relation type
STXBP5	TF binding region
STXBP5-AS1	TF binding region
STXBP5-AS1	CpG island
STXBP5	CpG island
ENSG00000227748	Chromatin interaction
ENSG00000196634	Chromatin interaction
ENSG00000231028	Chromatin interaction
ENSG00000135541	Chromatin interaction
ENSG00000233452	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2328812	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73788804	1.00[AMR][1000 genomes]
rs7761345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7763489	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019245	chr6:147350834-147609776	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538467	chr6:147350834-147609776	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886752	chr6:147443480-147729477	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1820434	chr6:147518489-147543262	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3387409	chr6:147524059-147526607	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3338422	chr6:147524084-147526632	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 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	chr6:147522800-147526200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
2	chr6:147522800-147528600	Active TSS	Duodenum Mucosa	Duodenum
3	chr6:147522800-147529000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:147523000-147525800	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr6:147523000-147525800	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr6:147523000-147526000	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:147523000-147526000	Active TSS	Fetal Kidney	kidney
8	chr6:147523000-147526200	Active TSS	Colon Smooth Muscle	Colon
9	chr6:147523000-147526200	Active TSS	Esophagus	oesophagus
10	chr6:147523000-147526200	Active TSS	Fetal Lung	lung
11	chr6:147523000-147526200	Active TSS	Placenta Amnion	Placenta Amnion
12	chr6:147523000-147526400	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr6:147523000-147526400	Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr6:147523000-147526400	Active TSS	Stomach Mucosa	stomach
15	chr6:147523000-147526600	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr6:147523000-147526800	Active TSS	Brain Substantia Nigra	brain
17	chr6:147523000-147526800	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr6:147523000-147526800	Active TSS	Fetal Brain Male	brain
19	chr6:147523000-147527000	Active TSS	H1 Cell Line	embryonic stem cell
20	chr6:147523000-147527000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:147523000-147527000	Active TSS	Fetal Stomach	stomach
22	chr6:147523000-147527000	Active TSS	Psoas Muscle	Psoas
23	chr6:147523000-147527000	Active TSS	Rectal Smooth Muscle	rectum
24	chr6:147523000-147527000	Active TSS	Thymus	Thymus
25	chr6:147523000-147527000	Active TSS	GM12878-XiMat	blood
26	chr6:147523000-147527000	Active TSS	NH-A	brain
27	chr6:147523000-147527200	Active TSS	Colonic Mucosa	Colon
28	chr6:147523000-147527200	Active TSS	A549	lung
29	chr6:147523000-147527400	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr6:147523000-147527400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:147523000-147527400	Active TSS	Fetal Intestine Small	intestine
32	chr6:147523000-147527600	Active TSS	Fetal Intestine Large	intestine
33	chr6:147523000-147527800	Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr6:147523000-147528000	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr6:147523000-147528600	Active TSS	Brain Cingulate Gyrus	brain
36	chr6:147523000-147528800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:147523000-147528800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:147523000-147528800	Active TSS	Brain Anterior Caudate	brain
39	chr6:147523000-147528800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr6:147523000-147529000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:147523000-147529200	Active TSS	NHLF	lung
42	chr6:147523000-147529600	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr6:147523000-147529600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:147523000-147529800	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr6:147523200-147525800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:147523200-147526000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:147523200-147526000	Active TSS	Lung	lung
48	chr6:147523200-147526000	Active TSS	Pancreas	Pancrea
49	chr6:147523200-147526000	Active TSS	Spleen	Spleen
50	chr6:147523200-147526200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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