Variant report

Variant	rs1220418
Chromosome Location	chr1:9938819-9938820
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	chr1:9938807-9938833	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:9938308..9941102-chr1:9950921..9954538,4	MCF-7	breast:
2	chr1:9936836..9938925-chr1:9967640..9970664,3	MCF-7	breast:

Variant related genes	Relation type
CTNNBIP1	TF binding region
ENSG00000178585	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1220381	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1220382	0.88[EUR][1000 genomes]
rs1220383	0.81[CEU][hapmap]
rs1220384	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1220392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1220393	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1220394	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1220395	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1220396	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1220404	0.87[AMR][1000 genomes]
rs1220405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1220406	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1220411	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1220412	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1220413	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1372106	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1470160	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs15177	0.84[CHB][hapmap]
rs1660735	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17034420	0.84[CHB][hapmap]
rs2083577	0.87[EUR][1000 genomes]
rs2278611	0.84[CHB][hapmap]
rs2379108	0.88[EUR][1000 genomes]
rs2486084	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2582980	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2582981	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3120822	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3860318	0.84[CHB][hapmap]
rs3888014	0.84[CHB][hapmap]
rs6695334	0.84[CHB][hapmap]
rs7225	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs935073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935074	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs935075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs946275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
5	nsv871146	chr1:9897001-9951288	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv545380	chr1:9918183-9987007	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9904800-9946000	Weak transcription	Fetal Kidney	kidney
2	chr1:9918600-9943800	Weak transcription	Small Intestine	intestine
3	chr1:9927600-9941800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:9930200-9941800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr1:9930800-9942200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:9930800-9949600	Weak transcription	Fetal Lung	lung
7	chr1:9932000-9942400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:9932200-9941800	Weak transcription	Primary T cells from cord blood	blood
9	chr1:9932200-9942200	Weak transcription	Thymus	Thymus
10	chr1:9932200-9942800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:9932600-9942600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr1:9932600-9960200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:9932800-9942200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:9933000-9946000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:9935400-9940600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr1:9935400-9941800	Weak transcription	NHLF	lung
17	chr1:9935400-9942000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:9935400-9942600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:9935400-9942800	Weak transcription	Colonic Mucosa	Colon
20	chr1:9935400-9944200	Weak transcription	Ovary	ovary
21	chr1:9935400-9948800	Weak transcription	Primary B cells from cord blood	blood
22	chr1:9935600-9940600	Weak transcription	GM12878-XiMat	blood
23	chr1:9935600-9941000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr1:9935600-9941600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:9935600-9941600	Weak transcription	HSMM	muscle
26	chr1:9935600-9941800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:9935600-9941800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:9935600-9942200	Weak transcription	Lung	lung
29	chr1:9935600-9943400	Weak transcription	Pancreas	Pancrea
30	chr1:9935600-9948600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:9935600-9949200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr1:9935600-9949400	Weak transcription	HUVEC	blood vessel
33	chr1:9935600-9950200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:9935600-9960800	Weak transcription	Fetal Intestine Large	intestine
35	chr1:9935800-9940600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:9935800-9942000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:9935800-9944200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:9935800-9946200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:9935800-9946600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:9935800-9950800	Weak transcription	Aorta	Aorta
41	chr1:9936000-9940800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:9936000-9941600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr1:9936000-9941800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:9936000-9943000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr1:9936000-9946200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:9936000-9948800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr1:9936000-9950000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:9936000-9950000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr1:9936200-9949800	Weak transcription	Colon Smooth Muscle	Colon
50	chr1:9936400-9939600	Strong transcription	Fetal Intestine Small	intestine

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