Variant report

Variant	rs72699961
Chromosome Location	chr1:165799140-165799141
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	MXI1	chr1:165795790-165799461	SK-N-SH	brain:	n/a	n/a
2	TBL1XR1	chr1:165796917-165799236	K562	blood:	n/a	n/a
3	POLR2A	chr1:165796645-165799245	MCF10A-Er-Src	breast:	n/a	n/a
4	IRF1	chr1:165796469-165799244	K562	blood:	n/a	chr1:165797613-165797627 chr1:165798461-165798475 chr1:165798553-165798564
5	POLR2A	chr1:165796639-165799261	GM12878	blood:	n/a	n/a
6	GATA1	chr1:165796191-165799199	PBDE	blood:	n/a	chr1:165796537-165796544 chr1:165796555-165796565 chr1:165796530-165796551 chr1:165796537-165796544 chr1:165796537-165796544 chr1:165796268-165796278
7	HEY1	chr1:165796685-165799262	K562	blood:	n/a	chr1:165797282-165797297 chr1:165797294-165797309 chr1:165796793-165796808 chr1:165797609-165797624 chr1:165797010-165797025 chr1:165797590-165797605 chr1:165797178-165797193 chr1:165797231-165797246
8	POLR2A	chr1:165799128-165799198	H1-hESC	embryonic stem cell:	n/a	n/a
9	CHD1	chr1:165796874-165799140	GM12878	blood:	n/a	chr1:165797014-165797024 chr1:165797585-165797595 chr1:165797665-165797675
10	POLR2A	chr1:165796751-165799163	K562	blood:	n/a	n/a
11	WRNIP1	chr1:165798265-165799442	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:165796648-165799345	IMR90	lung:	n/a	n/a
13	TEAD4	chr1:165797381-165799148	K562	blood:	n/a	n/a
14	POLR2A	chr1:165797312-165799305	A549	lung:	n/a	n/a
15	CHD1	chr1:165796053-165799451	IMR90	lung:	n/a	chr1:165797014-165797024 chr1:165796765-165796775 chr1:165797585-165797595 chr1:165797665-165797675

No.	Distal block	Cell Line	Cell type
1	chr1:165685761..165688091-chr1:165797394..165800120,2	K562	blood:
2	chr1:165798053..165799867-chr1:165811993..165814835,2	MCF-7	breast:
3	chr1:165735886..165744990-chr1:165791702..165805629,42	K562	blood:
4	chr1:165797467..165799152-chr1:165835828..165838379,2	MCF-7	breast:
5	chr1:165741744..165743826-chr1:165797591..165799642,2	MCF-7	breast:
6	chr1:165667556..165669480-chr1:165798614..165800246,2	K562	blood:
7	chr1:165778822..165780861-chr1:165797146..165799667,2	MCF-7	breast:
8	chr1:165797029..165799386-chr1:165863557..165867019,3	K562	blood:
9	chr1:165797327..165800051-chr1:165876668..165879627,3	MCF-7	breast:
10	chr1:165733730..165736417-chr1:165798667..165800425,2	K562	blood:
11	chr1:165736117..165742504-chr1:165795129..165799551,11	MCF-7	breast:
12	chr1:165798709..165800702-chr6:26239289..26241961,2	MCF-7	breast:
13	chr1:165598807..165601582-chr1:165797127..165800019,4	K562	blood:
14	chr1:165795260..165799386-chr1:165863983..165867487,4	K562	blood:
15	chr1:165736523..165741866-chr1:165791420..165802380,26	K562	blood:

Variant related genes	Relation type
TMCO1	TF binding region
ENSG00000143183	Chromatin interaction
ENSG00000143198	Chromatin interaction
ENSG00000215838	Chromatin interaction
ENSG00000143179	Chromatin interaction
ENSG00000143149	Chromatin interaction
ENSG00000198327	Chromatin interaction
ENSG00000224358	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12079614	0.93[ASN][1000 genomes]
rs7534738	0.93[ASN][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	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1011720	chr1:165669589-165802516	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv517792	chr1:165785503-165811729	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
4	esv2830094	chr1:165785503-165840411	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	nsv818544	chr1:165797966-165811729	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
6	nsv548097	chr1:165797966-165825166	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72699961	RP11-466F5.8	cis	Artery Tibial	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165796000-165799200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr1:165796200-165799200	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr1:165796400-165799200	Active TSS	H9 Cell Line	embryonic stem cell
4	chr1:165796400-165799200	Active TSS	GM12878-XiMat	blood
5	chr1:165796400-165799400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:165796400-165799400	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr1:165796400-165799400	Active TSS	HSMMtube	muscle
8	chr1:165796400-165800000	Active TSS	Psoas Muscle	Psoas
9	chr1:165796600-165799200	Active TSS	H1 Cell Line	embryonic stem cell
10	chr1:165796600-165799200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:165796600-165799200	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr1:165796600-165799200	Active TSS	A549	lung
13	chr1:165796600-165799400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:165796600-165799400	Active TSS	NHLF	lung
15	chr1:165797400-165799200	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr1:165797800-165799200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:165797800-165799400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:165798200-165799200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:165798400-165799200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr1:165798400-165799200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr1:165798400-165799200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr1:165798400-165799200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:165798400-165802200	Weak transcription	Left Ventricle	heart
24	chr1:165798600-165799200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:165798600-165799200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:165798600-165799200	Flanking Active TSS	Brain Germinal Matrix	brain
27	chr1:165798600-165799400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr1:165798600-165799400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:165798600-165799400	Flanking Active TSS	Fetal Brain Female	brain
30	chr1:165798600-165799400	Enhancers	Small Intestine	intestine
31	chr1:165798600-165799400	Enhancers	Stomach Mucosa	stomach
32	chr1:165798600-165799400	Flanking Active TSS	NHEK	skin
33	chr1:165798600-165801000	Transcr. at gene 5' and 3'	Dnd41	blood
34	chr1:165798600-165802200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:165798600-165811000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr1:165798800-165799200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:165798800-165799200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:165798800-165799200	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr1:165798800-165799200	Enhancers	Colonic Mucosa	Colon
40	chr1:165798800-165799200	Active TSS	Fetal Thymus	thymus
41	chr1:165798800-165799200	Weak transcription	Gastric	stomach
42	chr1:165798800-165799200	Enhancers	Stomach Smooth Muscle	stomach
43	chr1:165798800-165799200	Flanking Active TSS	NHDF-Ad	bronchial
44	chr1:165798800-165799400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:165798800-165799400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr1:165798800-165799400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr1:165798800-165799400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:165798800-165799400	Enhancers	Fetal Muscle Leg	muscle
49	chr1:165798800-165799400	Enhancers	Pancreas	Pancrea
50	chr1:165798800-165799400	Enhancers	Sigmoid Colon	Sigmoid Colon

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