Variant report

Variant	rs1200105
Chromosome Location	chr1:169056398-169056399
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	RFX5	chr1:169056372-169056668	HepG2	liver:	n/a	chr1:169056481-169056496
2	EP300	chr1:169056336-169056582	GM12878	blood:	n/a	n/a
3	REST	chr1:169055991-169056819	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr1:169056122-169056752	H1-neurons	neurons:	n/a	n/a
5	RFX5	chr1:169056371-169056544	GM12878	blood:	n/a	chr1:169056481-169056496
6	REST	chr1:169055770-169057522	H1-neurons	neurons:	n/a	n/a
7	EP300	chr1:169056356-169056651	HepG2	liver:	n/a	n/a
8	ARID3A	chr1:169055838-169056604	HepG2	liver:	n/a	n/a
9	GATA2	chr1:169054834-169056675	SH-SY5Y	brain:	n/a	chr1:169055364-169055371 chr1:169055364-169055371 chr1:169055364-169055371
10	POLR2A	chr1:169055967-169056837	H1-neurons	neurons:	n/a	n/a
11	RFX5	chr1:169055481-169056920	SK-N-SH	brain:	n/a	chr1:169056481-169056496

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169055830..169060702-chr1:169073415..169077056,5	MCF-7	breast:
2	chr1:169053133..169065213-chr1:169070028..169077898,15	MCF-7	breast:

Variant related genes	Relation type
LINC00970	TF binding region
ENSG00000143153	Chromatin interaction
ENSG00000237707	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1040506	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1200089	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1200092	0.89[EUR][1000 genomes]
rs1200097	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1200099	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1200103	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1200106	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1200114	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1200115	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1200122	0.88[AMR][1000 genomes]
rs1200125	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1200128	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1320973	1.00[CHB][hapmap]
rs1575041	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1575042	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2982459	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2982461	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3007364	0.80[EUR][1000 genomes]
rs3007369	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3007370	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4656175	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs909926	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs932393	0.81[AFR][1000 genomes];0.88[AMR][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	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169054800-169056600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:169054800-169057200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:169054800-169057400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:169054800-169058600	Enhancers	Fetal Intestine Large	intestine
5	chr1:169055000-169057200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:169055000-169057200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:169055000-169057200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr1:169055000-169057200	Enhancers	HepG2	liver
9	chr1:169055000-169058000	Enhancers	Fetal Intestine Small	intestine
10	chr1:169055200-169056400	Enhancers	Small Intestine	intestine
11	chr1:169055200-169056600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr1:169055200-169056800	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr1:169055200-169057400	Enhancers	Primary hematopoietic stem cells	blood
14	chr1:169055200-169057400	Enhancers	Left Ventricle	heart
15	chr1:169055200-169058600	Enhancers	Brain Angular Gyrus	brain
16	chr1:169055200-169062200	Enhancers	Brain Anterior Caudate	brain
17	chr1:169055400-169060400	Enhancers	Brain Substantia Nigra	brain
18	chr1:169055800-169056400	Enhancers	Primary T cells fromperipheralblood	blood
19	chr1:169055800-169056400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:169055800-169056400	Enhancers	Right Atrium	heart
21	chr1:169055800-169056400	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr1:169055800-169056600	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr1:169055800-169056600	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr1:169055800-169056800	Flanking Active TSS	Fetal Heart	heart
25	chr1:169055800-169056800	Enhancers	Ovary	ovary
26	chr1:169055800-169057000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr1:169055800-169057000	Enhancers	Stomach Smooth Muscle	stomach
28	chr1:169055800-169057200	Enhancers	Primary T cells from cord blood	blood
29	chr1:169055800-169057400	Enhancers	Fetal Lung	lung
30	chr1:169055800-169057600	Enhancers	Duodenum Mucosa	Duodenum
31	chr1:169055800-169057600	Enhancers	Pancreas	Pancrea
32	chr1:169055800-169058000	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr1:169055800-169058000	Enhancers	Right Ventricle	heart
34	chr1:169055800-169058200	Enhancers	Colon Smooth Muscle	Colon
35	chr1:169056000-169056400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr1:169056000-169056400	Flanking Active TSS	Fetal Brain Female	brain
37	chr1:169056000-169056600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:169056000-169056600	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr1:169056000-169056600	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr1:169056000-169056800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:169056000-169056800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:169056000-169056800	Enhancers	Fetal Muscle Leg	muscle
43	chr1:169056000-169057200	Enhancers	Stomach Mucosa	stomach
44	chr1:169056000-169058200	Enhancers	Rectal Smooth Muscle	rectum
45	chr1:169056200-169056400	Enhancers	Aorta	Aorta
46	chr1:169056200-169056400	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr1:169056200-169056600	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr1:169056200-169056600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:169056200-169056600	Flanking Active TSS	Fetal Brain Male	brain
50	chr1:169056200-169056600	Enhancers	Pancreatic Islets	Pancreatic Islet

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