Variant report

Variant	rs11964560
Chromosome Location	chr6:87646919-87646920
allele	C/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	CEBPB	chr6:87646831-87647175	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr6:87646773-87647112	K562	blood:	n/a	chr6:87646950-87646962 chr6:87646947-87646966 chr6:87646953-87646962 chr6:87646950-87646963
3	CTCF	chr6:87646880-87647030	AG04450	lung:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
4	CTCF	chr6:87646624-87647301	A549	lung:	n/a	chr6:87647283-87647292 chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967 chr6:87646683-87646692
5	CTCF	chr6:87646879-87647049	Hela-S3	cervix:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
6	CTCF	chr6:87646813-87647115	GM12892	blood:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
7	CTCF	chr6:87646900-87647050	GM12875	blood:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
8	CHD2	chr6:87646571-87647107	H1-hESC	embryonic stem cell:	n/a	chr6:87646767-87646777
9	CTCF	chr6:87646840-87646990	MCF-7	breast:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
10	CTCF	chr6:87646860-87647010	AG09309	skin:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
11	CTCF	chr6:87646900-87647050	HEK293	kidney:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
12	CTCF	chr6:87646900-87647050	HVMF	connective:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
13	ZNF143	chr6:87646833-87647109	K562	blood:	n/a	n/a
14	YY1	chr6:87646606-87647188	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr6:87646880-87647030	AG09319	gingival:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
16	CTCF	chr6:87646894-87647060	Lung_OC	lung:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
17	RAD21	chr6:87646656-87647189	HepG2	liver:	n/a	chr6:87646950-87646962 chr6:87646947-87646966 chr6:87646953-87646962 chr6:87646950-87646963
18	YY1	chr6:87646781-87647175	HepG2	liver:	n/a	n/a
19	RAD21	chr6:87646729-87647214	HCT-116	colon:	n/a	chr6:87646950-87646962 chr6:87646947-87646966 chr6:87646953-87646962 chr6:87646950-87646963
20	CTCF	chr6:87646900-87647050	AG04449	skin:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
21	CTCF	chr6:87646611-87647180	MCF-7	breast:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967 chr6:87646683-87646692
22	BRCA1	chr6:87646718-87646964	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr6:87646807-87647185	GM19238	blood:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
24	CTCF	chr6:87646860-87647010	GM12864	blood:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
25	RAD21	chr6:87646773-87647086	GM12878	blood:	n/a	chr6:87646950-87646962 chr6:87646947-87646966 chr6:87646953-87646962 chr6:87646950-87646963
26	CTCF	chr6:87646860-87647010	AG09319	gingival:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
27	CTCF	chr6:87646749-87647155	K562	blood:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
28	CTCF	chr6:87646880-87647030	GM12869	blood:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
29	YY1	chr6:87646811-87647041	GM12878	blood:	n/a	n/a
30	CTCF	chr6:87646880-87647030	RPTEC	kidney:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
31	CTCF	chr6:87646831-87647048	GM13976	blood:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
32	CTCF	chr6:87646788-87647362	MCF-7	breast:	n/a	chr6:87647283-87647292 chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
33	CTCF	chr6:87646521-87647762	SK-N-SH	brain:	n/a	chr6:87647283-87647292 chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967 chr6:87646683-87646692
34	TAF1	chr6:87646688-87647223	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr6:87646791-87647050	HepG2	liver:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
36	TBP	chr6:87646611-87647060	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr6:87646770-87647145	K562	blood:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
38	RAD21	chr6:87646744-87647157	HepG2	liver:	n/a	chr6:87646950-87646962 chr6:87646947-87646966 chr6:87646953-87646962 chr6:87646950-87646963
39	CTCF	chr6:87646860-87647010	GM06990	blood:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
40	RAD21	chr6:87646728-87647130	ECC-1	luminal epithelium:	n/a	chr6:87646950-87646962 chr6:87646947-87646966 chr6:87646953-87646962 chr6:87646950-87646963
41	ZNF143	chr6:87646811-87647123	GM12878	blood:	n/a	n/a
42	CTCF	chr6:87646860-87647010	GM12867	blood:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
43	CTCF	chr6:87646815-87647114	Medullo	brain:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
44	CTCF	chr6:87646880-87647030	HEEpiC	esophagus:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
45	CTCF	chr6:87646900-87647050	HPF	lung:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
46	E2F6	chr6:87646340-87647832	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr6:87646880-87647030	GM12871	blood:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
48	CTCF	chr6:87646826-87647093	SK-N-SH_RA	brain:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
49	CTCF	chr6:87646900-87647050	HBMEC	blood vessel:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967
50	CTCF	chr6:87646868-87647079	GM10248	blood:	n/a	chr6:87646954-87646962 chr6:87646944-87646965 chr6:87646949-87646967

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:87646876-87646926	NT2-D1	testis:	n/a
2	chr6:87646876-87646926	MCF10A-Er-Src	breast:	n/a
3	chr6:87646876-87646926	ProgFib	skin:	n/a
4	chr6:87646876-87646926	AG04449	skin:	fetal
5	chr6:87646876-87646926	SK-N-MC	brain:	n/a
6	chr6:87646876-87646926	HCT-116	colon:	n/a
7	chr6:87646876-87646926	NB4	blood:	n/a
8	chr6:87646876-87646926	NHBE	bronchial:	n/a
9	chr6:87646876-87646926	AG09319	gingival:	n/a
10	chr6:87646876-87646926	SKMC	muscle:	n/a
11	chr6:87646876-87646926	AG04450	lung:	fetal
12	chr6:87646876-87646926	PANC-1	pancreas:	n/a
13	chr6:87646876-87646926	HEK293	kidney:	embryo
14	chr6:87646876-87646926	HEEpiC	esophagus:	n/a
15	chr6:87646876-87646926	RPTEC	kidney:	n/a
16	chr6:87646876-87646926	GM12892	blood:	n/a
17	chr6:87646876-87646926	GM19239	blood:	n/a
18	chr6:87646876-87646926	SAEC	small airway:	n/a
19	chr6:87646876-87646926	AG09309	skin:	n/a
20	chr6:87646876-87646926	A549	lung:	n/a
21	chr6:87646876-87646926	SK-N-SH	brain:	n/a
22	chr6:87646876-87646926	BJ	skin:	n/a
23	chr6:87646876-87646926	LNCaP	prostate:	n/a
24	chr6:87646876-87646926	HepG2	liver:	n/a
25	chr6:87646876-87646926	ECC-1	luminal epithelium:	n/a
26	chr6:87646876-87646926	T-47D	breast:	n/a
27	chr6:87646876-87646926	GM12878	blood:	n/a
28	chr6:87646876-87646926	HUVEC	blood vessel:	n/a
29	chr6:87646876-87646926	BE2_C	brain:	n/a
30	chr6:87646876-87646926	AG10803	skin:	n/a
31	chr6:87646876-87646926	Caco-2	colon:	n/a
32	chr6:87646876-87646926	HCF	heart:	n/a
33	chr6:87646876-87646926	PFSK-1	brain:	n/a
34	chr6:87646876-87646926	GM06990	blood:	n/a
35	chr6:87646876-87646926	GM12891	blood:	n/a
36	chr6:87646876-87646926	HMEC	breast:	n/a
37	chr6:87646876-87646926	NH-A	brain:	n/a
38	chr6:87646876-87646926	Hepatocyte	liver:	n/a
39	chr6:87646876-87646926	HRPEpiC	eye:	n/a
40	chr6:87646876-87646926	H1-hESC	embryonic stem cell:	embryo
41	chr6:87646876-87646926	U87	brain:	n/a
42	chr6:87646876-87646926	HNPCEpiC	eye:	n/a
43	chr6:87646876-87646926	CMK	blood:	n/a
44	chr6:87646876-87646926	HCPEpiC	choroid plexus:	n/a
45	chr6:87646876-87646926	MCF-7	breast:	n/a
46	chr6:87646876-87646926	HIPEpiC	eye:	n/a
47	chr6:87646876-87646926	AoSMC	blood vessel:	n/a
48	chr6:87646876-87646926	HRCEpiC	kidney:	n/a
49	chr6:87646876-87646926	HRE	kidney:	n/a
50	chr6:87646876-87646926	NHDF-neo	bronchial:	n/a

Variant related genes	Relation type
HTR1E	TF binding region
HTR1E	CpG island

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12525091	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.86[ASN][1000 genomes]
rs12525105	0.86[ASN][1000 genomes]
rs12529712	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16877989	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1819144	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap]
rs1950791	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2875501	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3763229	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3763230	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55973818	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72910588	0.86[ASN][1000 genomes]
rs72910598	0.86[ASN][1000 genomes]
rs72910602	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72912421	0.88[EUR][1000 genomes];0.90[ASN][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	nsv1018878	chr6:86778852-87691755	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1031639	chr6:86815397-87721507	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1024751	chr6:87433199-87908721	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11964560	ZNF292	cis	cerebellar cortex	BrainEAC
rs11964560	C6orf165	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87646200-87647800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
2	chr6:87646400-87647600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
3	chr6:87646400-87647600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:87646400-87647800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:87646400-87648000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr6:87646400-87648000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr6:87646600-87647000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:87646600-87647000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
9	chr6:87646600-87647000	Enhancers	Liver	Liver
10	chr6:87646600-87647000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
11	chr6:87646600-87647000	Bivalent Enhancer	Fetal Intestine Small	intestine
12	chr6:87646600-87647000	Bivalent Enhancer	Fetal Stomach	stomach
13	chr6:87646600-87647000	Flanking Active TSS	Ovary	ovary
14	chr6:87646600-87647000	Active TSS	Rectal Smooth Muscle	rectum
15	chr6:87646600-87647000	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
16	chr6:87646600-87647000	Flanking Bivalent TSS/Enh	Stomach Mucosa	stomach
17	chr6:87646600-87647000	Active TSS	HepG2	liver
18	chr6:87646600-87647000	Active TSS	K562	blood
19	chr6:87646600-87647200	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
20	chr6:87646600-87647400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:87646600-87647400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:87646600-87647400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
23	chr6:87646600-87647400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
24	chr6:87646600-87647400	Bivalent/Poised TSS	Brain Substantia Nigra	brain
25	chr6:87646600-87647400	Active TSS	Fetal Kidney	kidney
26	chr6:87646600-87647600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr6:87646600-87647600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:87646600-87647600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:87646600-87647600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
30	chr6:87646600-87647600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
31	chr6:87646600-87647600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:87646600-87647600	Bivalent Enhancer	Placenta	Placenta
33	chr6:87646600-87647800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr6:87646600-87647800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
35	chr6:87646600-87647800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
36	chr6:87646600-87647800	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr6:87646600-87648000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
38	chr6:87646600-87648000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
39	chr6:87646600-87648000	Active TSS	Gastric	stomach
40	chr6:87646600-87648200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:87646600-87648800	Active TSS	Brain Angular Gyrus	brain
42	chr6:87646600-87648800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
43	chr6:87646800-87647000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr6:87646800-87647000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
45	chr6:87646800-87647000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:87646800-87647000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:87646800-87647000	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
48	chr6:87646800-87647000	Bivalent Enhancer	Fetal Muscle Leg	muscle
49	chr6:87646800-87647000	Active TSS	Pancreas	Pancrea
50	chr6:87646800-87647000	Bivalent/Poised TSS	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links