Variant report

Variant	rs1288936
Chromosome Location	chr1:226849761-226849762
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:226849760-226849910	HBMEC	blood vessel:	n/a	n/a
2	CTCF	chr1:226849680-226849830	HCPEpiC	choroid plexus:	n/a	n/a
3	CTCF	chr1:226849680-226849830	HMF	breast:	n/a	n/a
4	POLR2A	chr1:226849570-226852709	IMR90	lung:	n/a	n/a
5	CTCF	chr1:226849640-226849790	GM12873	blood:	n/a	n/a
6	CTCF	chr1:226849720-226849870	SK-N-SH_RA	brain:	n/a	n/a
7	CTCF	chr1:226849760-226849910	HEEpiC	esophagus:	n/a	n/a
8	CTCF	chr1:226849760-226849910	HA-sp	spinal cord:	n/a	n/a
9	CTCF	chr1:226849680-226849830	SK-N-SH_RA	brain:	n/a	n/a
10	CTCF	chr1:226849680-226849830	HRPEpiC	eye:	n/a	n/a
11	JUND	chr1:226849337-226851323	SK-N-SH	brain:	n/a	chr1:226850628-226850638 chr1:226850627-226850639 chr1:226850629-226850638 chr1:226850628-226850638 chr1:226850627-226850638 chr1:226850628-226850638
12	CTCF	chr1:226849720-226849870	BJ	skin:	n/a	n/a
13	CTCF	chr1:226849740-226849890	GM12866	blood:	n/a	n/a
14	CTCF	chr1:226849680-226849830	AG10803	skin:	n/a	n/a
15	CTCF	chr1:226849700-226849850	GM12865	blood:	n/a	n/a
16	MXI1	chr1:226849152-226851361	IMR90	lung:	n/a	n/a
17	CTCF	chr1:226849620-226849770	AG09319	gingival:	n/a	n/a
18	CTCF	chr1:226849700-226849850	HEK293	kidney:	n/a	n/a
19	CTCF	chr1:226849660-226849810	AoAF	blood vessel:	n/a	n/a
20	CTCF	chr1:226849620-226849770	HAc	cerebellar:	n/a	n/a
21	CTCF	chr1:226849620-226849770	HMF	breast:	n/a	n/a
22	NRF1	chr1:226849394-226851070	SK-N-SH	brain:	n/a	n/a
23	CTCF	chr1:226849680-226849830	NHDF-neo	bronchial:	n/a	n/a
24	CTCF	chr1:226849720-226849870	BE2_C	brain:	n/a	n/a
25	CTCF	chr1:226849740-226849890	HMEC	breast:	n/a	n/a
26	CTCF	chr1:226849640-226849790	AG10803	skin:	n/a	n/a
27	CTCF	chr1:226849720-226849870	NHEK	skin:	n/a	n/a
28	CTCF	chr1:226849740-226849890	HA-sp	spinal cord:	n/a	n/a
29	CTCF	chr1:226849700-226849850	HMEC	breast:	n/a	n/a
30	CTCF	chr1:226849740-226849890	HepG2	liver:	n/a	n/a
31	CTCF	chr1:226849691-226849930	IMR90	lung:	n/a	n/a
32	CTCF	chr1:226849740-226849890	AG04449	skin:	n/a	n/a
33	CTCF	chr1:226849700-226849850	HPF	lung:	n/a	n/a
34	CTCF	chr1:226849709-226849874	Medullo	brain:	n/a	n/a
35	CTCF	chr1:226849660-226849810	BE2_C	brain:	n/a	n/a
36	CTCF	chr1:226849700-226849850	NHDF-neo	bronchial:	n/a	n/a
37	RAD21	chr1:226849627-226849986	H1-hESC	embryonic stem cell:	n/a	chr1:226849784-226849791 chr1:226849635-226849649

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226841585..226843575-chr1:226849581..226851350,2	MCF-7	breast:
2	chr1:226848680..226852398-chr1:226863556..226867477,3	MCF-7	breast:
3	chr1:226849475..226852007-chr1:226878804..226881377,2	K562	blood:
4	chr1:226847991..226850832-chr1:226852889..226855644,2	MCF-7	breast:

No data

Variant related genes	Relation type
ITPKB-IT1	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10495246	0.85[JPT][hapmap]
rs1070361	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1071530	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1144838	0.85[JPT][hapmap]
rs1144839	0.83[JPT][hapmap]
rs1144840	0.85[JPT][hapmap]
rs1151804	0.85[JPT][hapmap]
rs1288938	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1288939	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17522524	0.85[JPT][hapmap]
rs17588687	0.92[JPT][hapmap]
rs3768376	0.92[JPT][hapmap]
rs3768393	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs3768396	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3820635	0.85[JPT][hapmap]
rs3820637	0.83[JPT][hapmap]
rs3820640	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs697847	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs708766	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[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	nsv873234	chr1:226779449-226859676	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv873235	chr1:226819073-226851963	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226836800-226856200	Enhancers	Left Ventricle	heart
2	chr1:226837000-226849800	Enhancers	Duodenum Smooth Muscle	Duodenum
3	chr1:226837400-226856200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:226837400-226856600	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr1:226837400-226856600	Enhancers	Brain Substantia Nigra	brain
6	chr1:226839400-226856200	Enhancers	Fetal Muscle Leg	muscle
7	chr1:226840600-226851800	Enhancers	Adipose Nuclei	Adipose
8	chr1:226840600-226852600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:226840600-226852800	Enhancers	Primary hematopoietic stem cells	blood
10	chr1:226841800-226850200	Enhancers	Psoas Muscle	Psoas
11	chr1:226841800-226856200	Enhancers	Brain Angular Gyrus	brain
12	chr1:226841800-226860600	Enhancers	Brain Cingulate Gyrus	brain
13	chr1:226842200-226850600	Enhancers	Pancreas	Pancrea
14	chr1:226842200-226852400	Enhancers	Esophagus	oesophagus
15	chr1:226843200-226850200	Genic enhancers	Fetal Thymus	thymus
16	chr1:226843400-226849800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:226843400-226850400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:226843400-226850400	Genic enhancers	Primary B cells from peripheral blood	blood
19	chr1:226843800-226854400	Enhancers	Brain Hippocampus Middle	brain
20	chr1:226844200-226850400	Genic enhancers	Primary T cells fromperipheralblood	blood
21	chr1:226844400-226850600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:226844800-226852400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:226845000-226850000	Genic enhancers	Primary T cells from cord blood	blood
24	chr1:226845400-226849800	Weak transcription	Osteobl	bone
25	chr1:226845400-226850200	Weak transcription	Fetal Kidney	kidney
26	chr1:226845600-226855600	Enhancers	Placenta	Placenta
27	chr1:226846000-226852200	Enhancers	Right Ventricle	heart
28	chr1:226846000-226852200	Genic enhancers	Thymus	Thymus
29	chr1:226846200-226850000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:226846200-226853000	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr1:226846200-226862400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:226846400-226849800	Genic enhancers	Fetal Stomach	stomach
33	chr1:226846400-226850000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:226846400-226850400	Enhancers	Brain Anterior Caudate	brain
35	chr1:226846600-226850200	Enhancers	Lung	lung
36	chr1:226846600-226852200	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr1:226846800-226850600	Enhancers	Duodenum Mucosa	Duodenum
38	chr1:226846800-226851800	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr1:226846800-226853000	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr1:226846800-226853000	Enhancers	Colonic Mucosa	Colon
41	chr1:226846800-226854000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:226847000-226852800	Enhancers	Fetal Lung	lung
43	chr1:226847000-226853000	Enhancers	Spleen	Spleen
44	chr1:226847200-226850200	Enhancers	Ovary	ovary
45	chr1:226847200-226856200	Enhancers	Fetal Muscle Trunk	muscle
46	chr1:226847400-226851000	Enhancers	Fetal Heart	heart
47	chr1:226847600-226849800	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr1:226847600-226850200	Enhancers	Small Intestine	intestine
49	chr1:226847600-226850200	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr1:226847600-226850400	Enhancers	Placenta Amnion	Placenta Amnion

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