Variant report

Variant	rs16941271
Chromosome Location	chr17:45001129-45001130
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	POLR2A	chr17:44999879-45001196	HepG2	liver:	n/a	n/a
2	POLR2A	chr17:44999993-45001134	GM12878	blood:	n/a	n/a
3	POLR2A	chr17:44999905-45001314	MCF10A-Er-Src	breast:	n/a	n/a
4	MXI1	chr17:44999866-45001475	IMR90	lung:	n/a	n/a
5	MAZ	chr17:44999883-45001369	IMR90	lung:	n/a	chr17:45000630-45000641 chr17:45000791-45000800
6	SIN3A	chr17:45000007-45001189	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr17:44999853-45001361	SK-N-SH	brain:	n/a	n/a
8	GABPA	chr17:44999850-45001269	SK-N-SH	brain:	n/a	chr17:45000606-45000615
9	GABPA	chr17:44999862-45001210	A549	lung:	n/a	chr17:45000606-45000615
10	ARID3A	chr17:44999979-45001207	HepG2	liver:	n/a	n/a
11	MAX	chr17:44999847-45001159	A549	lung:	n/a	chr17:45000630-45000641 chr17:45000791-45000800
12	POLR2A	chr17:45000309-45001253	HepG2	liver:	n/a	n/a
13	MXI1	chr17:44999657-45002150	SK-N-SH	brain:	n/a	n/a
14	GABPA	chr17:44999779-45001383	MCF-7	breast:	n/a	chr17:45001268-45001277 chr17:45000606-45000615
15	POLR2A	chr17:44999979-45001237	MCF10A-Er-Src	breast:	n/a	n/a
16	IRF1	chr17:44999980-45001227	K562	blood:	n/a	chr17:45000476-45000496
17	POLR2A	chr17:44999989-45001900	IMR90	lung:	n/a	n/a
18	POLR2A	chr17:44999991-45001199	HepG2	liver:	n/a	n/a
19	ELK4	chr17:45000111-45001144	Hela-S3	cervix:	n/a	chr17:45000473-45000482 chr17:45000473-45000481
20	TCF12	chr17:44999824-45001147	A549	lung:	n/a	chr17:44999958-44999968

No.	Distal block	Cell Line	Cell type
1	chr17:45000610..45002133-chr17:45017223..45020134,3	MCF-7	breast:
2	chr17:44999992..45001971-chr17:45015932..45018557,3	MCF-7	breast:
3	chr17:44995313..44999079-chr17:44999263..45002356,3	MCF-7	breast:
4	chr17:45000734..45002965-chr17:45025082..45026604,2	K562	blood:
5	chr15:44089561..44091456-chr17:44999592..45001929,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261886	TF binding region
ENSG00000210709	Chromatin interaction
ENSG00000184716	Chromatin interaction
ENSG00000108433	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10491148	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11871306	1.00[CEU][hapmap]
rs1638450	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs16941273	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16941300	1.00[CEU][hapmap]
rs16941306	1.00[CEU][hapmap];0.80[AFR][1000 genomes]
rs16941312	1.00[CEU][hapmap]
rs16941317	1.00[CEU][hapmap]
rs16941318	1.00[CEU][hapmap]
rs16941324	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16941373	1.00[AMR][1000 genomes]
rs16941378	1.00[AMR][1000 genomes]
rs16941390	1.00[CEU][hapmap]
rs197910	0.90[EUR][1000 genomes]
rs197931	0.90[EUR][1000 genomes]
rs197935	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs197937	0.90[EUR][1000 genomes]
rs197944	0.90[EUR][1000 genomes]
rs7212691	1.00[EUR][1000 genomes]
rs73985103	0.90[EUR][1000 genomes]
rs754474	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs8082211	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking 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 miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv531823	chr17:44485771-45067769	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv908562	chr17:44828931-45102413	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv949295	chr17:44836653-45080757	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
8	nsv428672	chr17:44872446-45023425	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1067211	chr17:44979111-45057620	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
10	nsv543378	chr17:44979111-45057620	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:44999400-45001200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr17:44999400-45001400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:44999600-45001200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr17:44999600-45001200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr17:44999600-45001200	Active TSS	Brain Anterior Caudate	brain
6	chr17:44999600-45001200	Active TSS	Brain Cingulate Gyrus	brain
7	chr17:44999600-45001200	Active TSS	Duodenum Mucosa	Duodenum
8	chr17:44999600-45001200	Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr17:44999600-45001400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr17:44999600-45001400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr17:44999600-45001400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr17:44999600-45001400	Active TSS	Stomach Smooth Muscle	stomach
13	chr17:44999600-45001800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr17:44999600-45002000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr17:44999600-45002200	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr17:44999800-45001200	Active TSS	Primary T cells fromperipheralblood	blood
17	chr17:44999800-45001200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr17:44999800-45001200	Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr17:44999800-45001200	Active TSS	Brain Germinal Matrix	brain
20	chr17:44999800-45001200	Active TSS	Brain Hippocampus Middle	brain
21	chr17:44999800-45001200	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr17:44999800-45001200	Active TSS	Fetal Muscle Leg	muscle
23	chr17:44999800-45001200	Active TSS	Placenta	Placenta
24	chr17:44999800-45001200	Active TSS	Fetal Stomach	stomach
25	chr17:44999800-45001200	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr17:44999800-45001200	Active TSS	Dnd41	blood
27	chr17:44999800-45001200	Active TSS	HUVEC	blood vessel
28	chr17:44999800-45001200	Active TSS	NH-A	brain
29	chr17:44999800-45001200	Active TSS	NHEK	skin
30	chr17:44999800-45001400	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr17:44999800-45001400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr17:44999800-45001400	Active TSS	H9 Cell Line	embryonic stem cell
33	chr17:44999800-45001400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr17:44999800-45001400	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr17:44999800-45001400	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr17:44999800-45001400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr17:44999800-45001400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr17:44999800-45001400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr17:44999800-45001400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr17:44999800-45001400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr17:44999800-45001400	Active TSS	Muscle Satellite Cultured Cells	--
42	chr17:44999800-45001400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr17:44999800-45001400	Active TSS	Brain Angular Gyrus	brain
44	chr17:44999800-45001400	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr17:44999800-45001400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr17:44999800-45001400	Active TSS	Colonic Mucosa	Colon
47	chr17:44999800-45001400	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr17:44999800-45001400	Active TSS	Fetal Muscle Trunk	muscle
49	chr17:44999800-45001400	Active TSS	Left Ventricle	heart
50	chr17:44999800-45001400	Active TSS	Placenta Amnion	Placenta Amnion

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