Variant report

Variant	rs72869669
Chromosome Location	chr1:9711631-9711632
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	NFIC	chr1:9711348-9711797	GM12878	blood:	n/a	n/a
2	TBL1XR1	chr1:9711428-9712144	GM12878	blood:	n/a	n/a
3	TBP	chr1:9711304-9711887	GM12878	blood:	n/a	n/a
4	PML	chr1:9710705-9715855	GM12878	blood:	n/a	n/a
5	CTCF	chr1:9711580-9711730	GM12874	blood:	n/a	n/a
6	CTCF	chr1:9711568-9711672	GM12891	blood:	n/a	n/a
7	MTA3	chr1:9711119-9712015	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:9711621-9712385	GM12891	blood:	n/a	n/a
9	TAF1	chr1:9711619-9711891	GM12878	blood:	n/a	n/a
10	CTCF	chr1:9711540-9711690	K562	blood:	n/a	n/a
11	HA-E2F1	chr1:9711286-9712213	MCF-7	breast:	n/a	chr1:9712069-9712079 chr1:9711941-9711950 chr1:9711510-9711517 chr1:9711648-9711657 chr1:9712136-9712146
12	EP300	chr1:9711488-9711891	GM12878	blood:	n/a	n/a
13	STAT5A	chr1:9710938-9711811	GM12878	blood:	n/a	chr1:9711702-9711713 chr1:9711454-9711466
14	MAX	chr1:9711553-9711855	NB4	blood:	n/a	n/a
15	POLR2A	chr1:9711536-9712728	GM12892	blood:	n/a	n/a
16	SPI1	chr1:9711483-9711944	HL-60	blood:	n/a	chr1:9711889-9711902
17	MAX	chr1:9711494-9711879	GM12878	blood:	n/a	n/a
18	CTCF	chr1:9711540-9711690	GM12868	blood:	n/a	n/a
19	POLR2A	chr1:9711491-9714825	GM15510	blood:	n/a	n/a
20	TAF1	chr1:9711519-9711922	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:9711194-9716883	GM12878	blood:	n/a	n/a
22	CTCF	chr1:9711584-9711667	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr1:9711334-9715731	GM19099	blood:	n/a	n/a
24	CTCF	chr1:9711500-9711650	HCT-116	colon:	n/a	n/a
25	POLR2A	chr1:9710881-9716735	GM12878	blood:	n/a	n/a
26	MXI1	chr1:9711320-9714837	GM12878	blood:	n/a	n/a
27	BCL3	chr1:9711545-9712572	GM12878	blood:	n/a	chr1:9712168-9712181 chr1:9711649-9711658
28	POLR2A	chr1:9711627-9713081	GM10847	blood:	n/a	n/a
29	POLR2A	chr1:9711350-9715716	GM18951	blood:	n/a	n/a
30	MAZ	chr1:9711269-9712016	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:9711303-9712023	H1-neurons	neurons:	n/a	n/a
32	MYC	chr1:9711593-9713280	NB4	blood:	n/a	chr1:9712065-9712075
33	POLR2A	chr1:9711182-9716568	GM12878	blood:	n/a	n/a
34	POLR2A	chr1:9711251-9715714	GM19193	blood:	n/a	n/a
35	SPI1	chr1:9711584-9711906	GM12891	blood:	n/a	chr1:9711889-9711902
36	CTCF	chr1:9711420-9711710	GM06990	blood:	n/a	n/a
37	POLR2A	chr1:9711295-9715892	GM12892	blood:	n/a	n/a
38	YY1	chr1:9711481-9711958	GM12878	blood:	n/a	chr1:9711648-9711657
39	RUNX3	chr1:9711386-9711908	GM12878	blood:	n/a	n/a
40	STAT1	chr1:9711366-9711753	GM12878	blood:	n/a	chr1:9711702-9711713 chr1:9711454-9711466
41	CTCF	chr1:9711575-9711673	GM19239	blood:	n/a	n/a
42	CTCF	chr1:9711520-9711670	GM06990	blood:	n/a	n/a
43	ELF1	chr1:9711494-9712019	GM12878	blood:	n/a	n/a
44	POLR2A	chr1:9711414-9712665	H1-neurons	neurons:	n/a	n/a
45	CTCF	chr1:9711576-9711655	MCF-7	breast:	n/a	n/a
46	SPI1	chr1:9711578-9711918	HL-60	blood:	n/a	chr1:9711889-9711902
47	CTCF	chr1:9711540-9711690	GM12864	blood:	n/a	n/a
48	POLR2A	chr1:9711245-9716266	GM18505	blood:	n/a	n/a
49	EBF1	chr1:9711512-9712168	GM12878	blood:	n/a	n/a
50	CTCF	chr1:9711580-9711730	HBMEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:9707217..9711639-chr1:9712091..9714173,4	K562	blood:
2	chr1:9710199..9713089-chr1:9746772..9748545,3	MCF-7	breast:
3	chr1:9711558..9713078-chr1:9714581..9716191,2	K562	blood:
4	chr1:9688707..9690744-chr1:9709792..9711665,2	K562	blood:

Variant related genes	Relation type
PIK3CD	TF binding region
ENSG00000179840	Chromatin interaction
ENSG00000171608	Chromatin interaction
ENSG00000231789	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs61412539	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72869644	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72869645	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72869651	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72869654	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72869655	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72869660	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7553125	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3397052	chr1:9711190-9713738	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9710800-9711800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr1:9710800-9711800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:9710800-9714800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr1:9711000-9711800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:9711000-9713200	Active TSS	GM12878-XiMat	blood
6	chr1:9711000-9714600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:9711200-9711800	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr1:9711200-9711800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
9	chr1:9711200-9711800	Flanking Active TSS	Fetal Thymus	thymus
10	chr1:9711200-9712600	Active TSS	Brain Anterior Caudate	brain
11	chr1:9711200-9712600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:9711200-9712800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
13	chr1:9711200-9713000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
14	chr1:9711200-9713000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr1:9711200-9713200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr1:9711200-9713200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr1:9711200-9713200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
18	chr1:9711400-9711800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:9711400-9711800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:9711400-9711800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:9711400-9711800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:9711400-9711800	Bivalent/Poised TSS	Colonic Mucosa	Colon
23	chr1:9711400-9711800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
24	chr1:9711400-9711800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
25	chr1:9711400-9711800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
26	chr1:9711400-9711800	Active TSS	HMEC	breast
27	chr1:9711400-9711800	Bivalent Enhancer	HUVEC	blood vessel
28	chr1:9711400-9711800	Flanking Bivalent TSS/Enh	NHEK	skin
29	chr1:9711400-9712000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:9711400-9712000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
31	chr1:9711400-9712000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
32	chr1:9711400-9712000	Active TSS	Right Ventricle	heart
33	chr1:9711400-9712200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:9711400-9712200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:9711400-9712200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:9711400-9712200	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr1:9711400-9712600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:9711400-9712600	Bivalent/Poised TSS	A549	lung
39	chr1:9711400-9712600	Active TSS	HSMMtube	muscle
40	chr1:9711400-9712800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
41	chr1:9711400-9712800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
42	chr1:9711400-9712800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:9711400-9712800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
44	chr1:9711400-9712800	Active TSS	HSMM	muscle
45	chr1:9711400-9713000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:9711400-9713200	Active TSS	Right Atrium	heart
47	chr1:9711400-9713800	Active TSS	Primary T cells from cord blood	blood
48	chr1:9711400-9713800	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr1:9711400-9714400	Active TSS	Brain Substantia Nigra	brain
50	chr1:9711600-9711800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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