Variant report

Variant	rs17034420
Chromosome Location	chr1:9938165-9938166
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:9936658..9938228-chr1:10092588..10094183,2	MCF-7	breast:
2	chr1:9936836..9938925-chr1:9967640..9970664,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178585	Chromatin interaction
ENSG00000130939	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11121499	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11809921	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1220392	0.84[CHB][hapmap]
rs1220396	0.84[CHB][hapmap]
rs1220405	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs1220408	0.95[ASN][1000 genomes]
rs1220412	0.82[CHD][hapmap]
rs1220418	0.84[CHB][hapmap]
rs15177	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2033960	0.86[EUR][1000 genomes]
rs2278611	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3860318	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3888014	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4417070	0.84[ASW][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs56315207	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57979292	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58281392	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59341676	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59530761	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59533551	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60389428	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60547803	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60624175	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61785229	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61785586	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61785590	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658583	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6660069	0.87[AMR][1000 genomes]
rs6681118	0.83[AMR][1000 genomes]
rs6683824	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686710	0.87[AMR][1000 genomes]
rs6695334	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72858042	0.87[AMR][1000 genomes]
rs72858053	0.87[AMR][1000 genomes]
rs72858068	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7533225	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs935073	0.84[CHB][hapmap];0.82[CHD][hapmap];0.83[LWK][hapmap]
rs935075	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs946275	0.84[CHB][hapmap]

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:98 , 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	chr1:9932400-9938200	Weak transcription	Gastric	stomach
12	chr1:9932600-9942600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:9932600-9960200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:9932800-9942200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:9933000-9946000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:9934600-9938800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:9934800-9938200	Enhancers	Fetal Heart	heart
18	chr1:9935000-9938800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:9935400-9940600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr1:9935400-9941800	Weak transcription	NHLF	lung
21	chr1:9935400-9942000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:9935400-9942600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:9935400-9942800	Weak transcription	Colonic Mucosa	Colon
24	chr1:9935400-9944200	Weak transcription	Ovary	ovary
25	chr1:9935400-9948800	Weak transcription	Primary B cells from cord blood	blood
26	chr1:9935600-9938200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:9935600-9940600	Weak transcription	GM12878-XiMat	blood
28	chr1:9935600-9941000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr1:9935600-9941600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:9935600-9941600	Weak transcription	HSMM	muscle
31	chr1:9935600-9941800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:9935600-9941800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:9935600-9942200	Weak transcription	Lung	lung
34	chr1:9935600-9943400	Weak transcription	Pancreas	Pancrea
35	chr1:9935600-9948600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:9935600-9949200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr1:9935600-9949400	Weak transcription	HUVEC	blood vessel
38	chr1:9935600-9950200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:9935600-9960800	Weak transcription	Fetal Intestine Large	intestine
40	chr1:9935800-9938200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:9935800-9940600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:9935800-9942000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:9935800-9944200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:9935800-9946200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:9935800-9946600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:9935800-9950800	Weak transcription	Aorta	Aorta
47	chr1:9936000-9938200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:9936000-9938200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:9936000-9940800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:9936000-9941600	Weak transcription	Muscle Satellite Cultured Cells	--

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