Variant report

Variant	rs17034775
Chromosome Location	chr1:10399008-10399009
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10269845..10271792-chr1:10397112..10399596,2	MCF-7	breast:
2	chr1:10269803..10271670-chr1:10397719..10399693,2	MCF-7	breast:
3	chr1:10397421..10400219-chr1:10415768..10418232,2	K562	blood:
4	chr1:10398291..10400779-chr1:10401590..10404208,2	MCF-7	breast:
5	chr1:10382347..10384488-chr1:10398364..10401134,2	K562	blood:

Variant related genes	Relation type
ENSG00000054523	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1046277	1.00[JPT][hapmap]
rs10492970	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11121524	0.82[JPT][hapmap]
rs11121551	0.80[ASW][hapmap]
rs12074936	0.82[JPT][hapmap]
rs1556916	0.80[ASW][hapmap]
rs1556917	0.80[ASW][hapmap]
rs17034569	0.82[JPT][hapmap]
rs17034591	0.88[ASN][1000 genomes]
rs17034601	0.88[ASN][1000 genomes]
rs17034615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17034616	0.88[ASN][1000 genomes]
rs17034627	0.88[ASN][1000 genomes]
rs17034655	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17034660	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17034716	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17034766	1.00[ASN][1000 genomes]
rs17034849	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2182326	0.80[ASW][hapmap]
rs2229688	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2297881	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3737154	0.88[ASN][1000 genomes]
rs3819096	1.00[ASN][1000 genomes]
rs41258245	0.88[ASN][1000 genomes]
rs4329521	0.88[ASN][1000 genomes]
rs4333852	0.80[ASW][hapmap]
rs4475756	0.80[ASW][hapmap]
rs4846195	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs57661717	0.88[ASN][1000 genomes]
rs57963032	0.82[ASN][1000 genomes]
rs61508659	0.94[ASN][1000 genomes]
rs72865913	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72865916	0.88[ASN][1000 genomes]
rs72865925	0.88[ASN][1000 genomes]
rs72865926	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72865927	0.88[ASN][1000 genomes]
rs72865941	0.88[ASN][1000 genomes]
rs72865946	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72865961	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72865963	0.84[AMR][1000 genomes]
rs72865999	1.00[ASN][1000 genomes]
rs72867415	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72867431	0.83[ASN][1000 genomes]
rs72867433	0.83[ASN][1000 genomes]
rs72867441	0.88[ASN][1000 genomes]
rs72867455	0.88[ASN][1000 genomes]
rs72867467	0.82[ASN][1000 genomes]
rs72867469	0.82[ASN][1000 genomes]
rs9783053	0.82[JPT][hapmap]

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	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv545381	chr1:10296452-10423988	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17034775	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10358800-10407000	Weak transcription	Primary B cells from cord blood	blood
2	chr1:10364600-10431000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:10379800-10399400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:10380200-10399800	Weak transcription	Stomach Mucosa	stomach
5	chr1:10380200-10404800	Weak transcription	Psoas Muscle	Psoas
6	chr1:10380400-10399600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:10380400-10436600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:10380600-10401000	Weak transcription	A549	lung
9	chr1:10380600-10426400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:10381000-10436400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:10385200-10436400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:10386000-10434800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:10386400-10403000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:10386400-10421600	Weak transcription	Hela-S3	cervix
15	chr1:10386600-10399800	Weak transcription	Fetal Lung	lung
16	chr1:10386800-10408600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:10393200-10415800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:10393200-10431200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:10393400-10402200	Strong transcription	Fetal Stomach	stomach
20	chr1:10393600-10430800	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr1:10393800-10406000	Strong transcription	Placenta	Placenta
22	chr1:10393800-10444600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:10394200-10399600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:10394200-10399800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:10394200-10400600	Strong transcription	Fetal Muscle Leg	muscle
26	chr1:10394200-10409800	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr1:10394200-10410000	Strong transcription	Fetal Brain Female	brain
28	chr1:10394200-10410000	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr1:10394200-10411400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:10394200-10413200	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:10394200-10414200	Strong transcription	Brain Germinal Matrix	brain
32	chr1:10394200-10414200	Strong transcription	Stomach Smooth Muscle	stomach
33	chr1:10394200-10415800	Strong transcription	Adipose Nuclei	Adipose
34	chr1:10394200-10415800	Strong transcription	Duodenum Mucosa	Duodenum
35	chr1:10394200-10441800	Strong transcription	Liver	Liver
36	chr1:10394400-10399200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr1:10394400-10399400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:10394400-10402400	Strong transcription	Pancreas	Pancrea
39	chr1:10394400-10404400	Strong transcription	Colon Smooth Muscle	Colon
40	chr1:10394400-10407000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:10394400-10409400	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:10394400-10410000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr1:10394400-10411200	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:10394400-10411400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:10394400-10413400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:10394400-10414200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr1:10394600-10405200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:10394800-10399400	Weak transcription	K562	blood
49	chr1:10394800-10401200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:10395000-10399800	Weak transcription	HMEC	breast

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