Variant report

Variant	rs12085485
Chromosome Location	chr1:47658709-47658710
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	CTCF	chr1:47658660-47658810	HA-sp	spinal cord:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658737-47658753
2	CHD2	chr1:47658049-47658820	HepG2	liver:	n/a	n/a
3	CTCF	chr1:47658640-47658790	WI-38	lung:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658737-47658753
4	CTCF	chr1:47658620-47658770	HA-sp	spinal cord:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658737-47658753
5	ELF1	chr1:47658460-47658984	K562	blood:	n/a	n/a
6	ELF1	chr1:47658331-47658924	GM12878	blood:	n/a	n/a
7	CTCF	chr1:47658660-47658810	Hela-S3	cervix:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658737-47658753
8	POLR2A	chr1:47657982-47658725	HepG2	liver:	n/a	n/a
9	RCOR1	chr1:47658552-47658889	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr1:47658589-47658898	MCF-7	breast:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658847-47658856 chr1:47658737-47658753
11	CTCF	chr1:47658566-47658933	ECC-1	luminal epithelium:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658847-47658856 chr1:47658737-47658753
12	MAX	chr1:47658524-47659125	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr1:47658621-47658873	A549	lung:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658847-47658856 chr1:47658737-47658753
14	CTCF	chr1:47658640-47658790	GM12801	blood:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658737-47658753
15	RAD21	chr1:47658609-47659027	MCF-7	breast:	n/a	chr1:47658737-47658756 chr1:47658742-47658752 chr1:47658738-47658747 chr1:47658738-47658752 chr1:47658742-47658754 chr1:47658736-47658750
16	SRF	chr1:47658514-47658969	K562	blood:	n/a	n/a
17	CTCF	chr1:47658598-47658902	GM10248	blood:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658847-47658856 chr1:47658737-47658753
18	GTF2F1	chr1:47658575-47658918	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr1:47657813-47659043	HepG2	liver:	n/a	n/a
20	CTCF	chr1:47658660-47658810	SK-N-SH_RA	brain:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658737-47658753
21	CTCF	chr1:47658680-47658830	BE2_C	brain:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658737-47658753
22	YY1	chr1:47658424-47659050	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr1:47658568-47658911	GM12878	blood:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658847-47658856 chr1:47658737-47658753
24	CTCF	chr1:47658660-47658810	AG10803	skin:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658737-47658753
25	RCOR1	chr1:47658413-47658999	K562	blood:	n/a	n/a
26	MAFK	chr1:47658536-47658982	K562	blood:	n/a	n/a
27	CTCF	chr1:47658660-47658810	BJ	skin:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658737-47658753
28	CTCF	chr1:47658533-47658934	H1-hESC	embryonic stem cell:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658847-47658856 chr1:47658737-47658753
29	ZNF143	chr1:47658557-47658925	GM12878	blood:	n/a	chr1:47658814-47658832
30	ZNF263	chr1:47658310-47658901	K562	blood:	n/a	chr1:47658376-47658385 chr1:47658567-47658576
31	CTCF	chr1:47658620-47658770	GM12864	blood:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658737-47658753
32	RAD21	chr1:47658510-47659008	MCF-7	breast:	n/a	chr1:47658737-47658756 chr1:47658742-47658752 chr1:47658738-47658747 chr1:47658738-47658752 chr1:47658514-47658527 chr1:47658742-47658754 chr1:47658736-47658750
33	HDAC2	chr1:47658282-47658909	HepG2	liver:	n/a	n/a
34	CTCF	chr1:47658580-47658730	A549	lung:	n/a	n/a
35	CTCF	chr1:47658660-47658810	MCF-7	breast:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658737-47658753
36	CTCF	chr1:47658680-47658830	HRE	kidney:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658737-47658753
37	CTCF	chr1:47658640-47658790	HFF-Myc	foreskin:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658737-47658753
38	YY1	chr1:47658451-47659016	HepG2	liver:	n/a	n/a
39	CTCF	chr1:47658660-47658810	GM12864	blood:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658737-47658753
40	CTCF	chr1:47658660-47658810	HMF	breast:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658737-47658753
41	RAD21	chr1:47658245-47658969	HepG2	liver:	n/a	chr1:47658737-47658756 chr1:47658742-47658752 chr1:47658738-47658747 chr1:47658738-47658752 chr1:47658514-47658527 chr1:47658742-47658754 chr1:47658736-47658750 chr1:47658255-47658264
42	STAT3	chr1:47658694-47658762	MCF10A-Er-Src	breast:	n/a	n/a
43	CUX1	chr1:47658346-47658965	K562	blood:	n/a	n/a
44	JUND	chr1:47658453-47658978	K562	blood:	n/a	n/a
45	CTCF	chr1:47658380-47659087	K562	blood:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658847-47658856 chr1:47658737-47658753
46	RAD21	chr1:47658481-47658956	A549	lung:	n/a	chr1:47658737-47658756 chr1:47658742-47658752 chr1:47658738-47658747 chr1:47658738-47658752 chr1:47658514-47658527 chr1:47658742-47658754 chr1:47658736-47658750
47	HCFC1	chr1:47658591-47658977	K562	blood:	n/a	n/a
48	CTCF	chr1:47658680-47658830	GM12872	blood:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658737-47658753
49	CTCF	chr1:47658680-47658830	HVMF	connective:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658737-47658753
50	CTCF	chr1:47658514-47658979	GM12878	blood:	n/a	chr1:47658739-47658747 chr1:47658739-47658752 chr1:47658736-47658754 chr1:47658736-47658749 chr1:47658738-47658759 chr1:47658847-47658856 chr1:47658737-47658753

No.	Distal block	Cell Line	Cell type
1	chr1:47658032..47658753-chr1:47728341..47729010,2	MCF-7	breast:
2	chr1:47644615..47645488-chr1:47658267..47659223,3	K562	blood:
3	chr1:47656717..47659062-chr1:47661249..47663518,2	K562	blood:
4	chr1:47658286..47659515-chr1:47727734..47729196,7	K562	blood:
5	chr1:47657045..47658805-chr1:47732419..47734234,2	K562	blood:
6	chr1:47658315..47659140-chr1:47728181..47729215,5	MCF-7	breast:
7	chr1:47656858..47659851-chr1:47734619..47737417,2	K562	blood:

Variant related genes	Relation type
PDZK1IP1	TF binding region
ENSG00000224805	Chromatin interaction
ENSG00000225506	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11488318	1.00[EUR][1000 genomes]
rs12072085	0.83[AMR][1000 genomes]
rs12072415	0.83[AMR][1000 genomes]
rs12092838	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56311064	1.00[EUR][1000 genomes]
rs58921777	1.00[EUR][1000 genomes]
rs59550357	1.00[EUR][1000 genomes]
rs60589829	1.00[EUR][1000 genomes]
rs61502427	1.00[EUR][1000 genomes]
rs72894542	1.00[EUR][1000 genomes]
rs72894554	1.00[EUR][1000 genomes]
rs72894561	1.00[EUR][1000 genomes]
rs72894575	1.00[EUR][1000 genomes]
rs74073558	1.00[EUR][1000 genomes]
rs74073585	1.00[EUR][1000 genomes]
rs74073742	1.00[EUR][1000 genomes]
rs74073791	1.00[EUR][1000 genomes]
rs74073793	1.00[EUR][1000 genomes]
rs74073879	1.00[EUR][1000 genomes]
rs74073880	1.00[EUR][1000 genomes]
rs74076309	1.00[EUR][1000 genomes]
rs74076312	1.00[EUR][1000 genomes]
rs74076314	1.00[EUR][1000 genomes]
rs74076315	1.00[EUR][1000 genomes]
rs74077366	1.00[EUR][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	nsv916813	chr1:47435635-47666179	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47652600-47659000	Enhancers	Fetal Intestine Small	intestine
2	chr1:47654600-47659200	Enhancers	Fetal Intestine Large	intestine
3	chr1:47655000-47659000	Enhancers	Lung	lung
4	chr1:47655000-47659200	Enhancers	Fetal Muscle Leg	muscle
5	chr1:47655200-47659000	Enhancers	Adipose Nuclei	Adipose
6	chr1:47655400-47658800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:47655400-47659400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:47655600-47659000	Enhancers	Placenta	Placenta
9	chr1:47655600-47659000	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr1:47655600-47659000	Enhancers	HSMMtube	muscle
11	chr1:47655600-47659200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:47655800-47658800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:47655800-47659000	Enhancers	Esophagus	oesophagus
14	chr1:47656000-47658800	Enhancers	Gastric	stomach
15	chr1:47656000-47659000	Enhancers	Stomach Mucosa	stomach
16	chr1:47656200-47660400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:47656400-47659000	Enhancers	Pancreas	Pancrea
18	chr1:47656600-47658800	Weak transcription	Brain Anterior Caudate	brain
19	chr1:47656600-47659000	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:47656800-47659000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr1:47657000-47659000	Enhancers	Ovary	ovary
22	chr1:47657200-47659000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:47657600-47658800	Enhancers	H1 Cell Line	embryonic stem cell
24	chr1:47657600-47658800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
25	chr1:47657600-47658800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
26	chr1:47657600-47659000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:47657600-47659400	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr1:47657800-47658800	Enhancers	Stomach Smooth Muscle	stomach
29	chr1:47657800-47659000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:47657800-47659000	Enhancers	Spleen	Spleen
31	chr1:47658000-47658800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:47658000-47658800	Enhancers	Liver	Liver
33	chr1:47658000-47658800	Flanking Active TSS	Colonic Mucosa	Colon
34	chr1:47658000-47658800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr1:47658000-47659000	Enhancers	Fetal Kidney	kidney
36	chr1:47658200-47658800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr1:47658200-47658800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:47658200-47659000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:47658200-47659000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:47658200-47659000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr1:47658200-47659000	Enhancers	Fetal Heart	heart
42	chr1:47658200-47659200	Enhancers	HUVEC	blood vessel
43	chr1:47658200-47659800	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr1:47658400-47658800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:47658400-47658800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:47658400-47658800	Enhancers	Brain Cingulate Gyrus	brain
47	chr1:47658400-47658800	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr1:47658400-47658800	Flanking Active TSS	K562	blood
49	chr1:47658400-47659000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
50	chr1:47658400-47659000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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