Variant report

Variant	rs2097081
Chromosome Location	chr4:2881109-2881110
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	chr4:2879534..2882793-chr4:2935370..2940285,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109736	Chromatin interaction
ENSG00000249673	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1012365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1242228	0.87[CHB][hapmap]
rs1263338	0.83[ASN][1000 genomes]
rs1263339	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1263342	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1263344	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1263345	0.94[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs1263347	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs1263349	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.81[ASN][1000 genomes]
rs1263359	0.95[CHB][hapmap]
rs1263360	0.90[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap]
rs12642795	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12645803	0.80[AMR][1000 genomes]
rs12650114	0.80[ASN][1000 genomes]
rs1419045	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs16843452	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16843523	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2051560	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2071695	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2185885	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2237004	0.94[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2239728	0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2282772	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2282773	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2282774	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2285084	0.94[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3775068	0.91[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3796469	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4690000	0.89[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4690001	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4690065	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4961	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4963	0.94[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4964	0.82[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap]
rs73082333	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73189458	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs762847	0.91[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap]
rs7654786	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7664801	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv521858	chr4:2846799-2881256	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv524060	chr4:2850142-2881256	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3383963	chr4:2877954-2882252	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2097081	DGKQ	cis	parietal	SCAN
rs2097081	ZNF732	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2870200-2914000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:2870600-2886000	Weak transcription	Fetal Brain Male	brain
3	chr4:2871000-2885800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr4:2871200-2881600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:2871200-2886000	Weak transcription	Aorta	Aorta
6	chr4:2871200-2896000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:2871200-2900600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:2872200-2890800	Weak transcription	A549	lung
9	chr4:2874000-2883600	Weak transcription	NH-A	brain
10	chr4:2874000-2887000	Weak transcription	Fetal Heart	heart
11	chr4:2874200-2900000	Weak transcription	Hela-S3	cervix
12	chr4:2875400-2886000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:2875800-2884200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr4:2876000-2881800	Strong transcription	Fetal Intestine Small	intestine
15	chr4:2876000-2884000	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:2876000-2885800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr4:2876000-2886000	Weak transcription	Colonic Mucosa	Colon
18	chr4:2876000-2886600	Weak transcription	Stomach Mucosa	stomach
19	chr4:2876400-2891600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:2876600-2882600	Strong transcription	Fetal Stomach	stomach
21	chr4:2876600-2889600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr4:2876600-2919200	Strong transcription	Primary B cells from peripheral blood	blood
23	chr4:2876800-2881800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:2876800-2889000	Strong transcription	GM12878-XiMat	blood
25	chr4:2876800-2889400	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr4:2876800-2891800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:2877000-2882000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:2877000-2882200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr4:2877000-2883600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr4:2877000-2883800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:2877000-2886000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr4:2877000-2889800	Strong transcription	Dnd41	blood
33	chr4:2877200-2882000	Strong transcription	Brain Germinal Matrix	brain
34	chr4:2877200-2882200	Strong transcription	Fetal Muscle Leg	muscle
35	chr4:2877200-2886200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr4:2877200-2891800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:2877200-2919400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:2877400-2882000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr4:2877400-2882000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:2877400-2882000	Strong transcription	Placenta	Placenta
41	chr4:2877400-2882000	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:2877400-2882000	Strong transcription	HepG2	liver
43	chr4:2877400-2882200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:2877400-2882400	Strong transcription	Primary hematopoietic stem cells	blood
45	chr4:2877400-2882400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:2877400-2882400	Strong transcription	Fetal Intestine Large	intestine
47	chr4:2877400-2882400	Strong transcription	Fetal Lung	lung
48	chr4:2877400-2884000	Weak transcription	Small Intestine	intestine
49	chr4:2877400-2886200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr4:2877400-2889600	Strong transcription	Liver	Liver

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