Variant report

Variant	rs7564410
Chromosome Location	chr2:233639909-233639910
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:233638966..233640656-chr2:233644513..233646533,2	MCF-7	breast:
2	chr2:233627414..233629760-chr2:233639796..233641450,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204120	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11883745	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11883794	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11884898	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11885497	0.95[EUR][1000 genomes]
rs11885646	0.97[EUR][1000 genomes]
rs11890879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11892326	0.85[CEU][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs11892639	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11894688	0.85[EUR][1000 genomes]
rs11897789	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11900295	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11900327	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11901015	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11904714	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2271702	0.83[EUR][1000 genomes]
rs2289913	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2289916	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2293781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305138	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2344614	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2880899	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34487721	0.83[EUR][1000 genomes]
rs3738904	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[EUR][1000 genomes]
rs3816336	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3817310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4144794	1.00[EUR][1000 genomes]
rs55686138	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55913849	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56140815	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56344253	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56357073	0.81[EUR][1000 genomes]
rs56953250	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57092158	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57211905	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57513852	0.83[EUR][1000 genomes]
rs57657135	0.98[EUR][1000 genomes]
rs57667610	0.83[EUR][1000 genomes]
rs57986228	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58268778	0.85[EUR][1000 genomes]
rs58466616	0.93[EUR][1000 genomes]
rs58520085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58835825	0.83[EUR][1000 genomes]
rs59488869	0.85[EUR][1000 genomes]
rs59502980	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59514271	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59667905	0.85[EUR][1000 genomes]
rs60103392	0.83[EUR][1000 genomes]
rs60532570	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61518838	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6719766	0.85[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs73092767	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73092790	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73102244	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73102257	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73102286	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73106355	0.83[EUR][1000 genomes]
rs73106363	0.85[EUR][1000 genomes]
rs73107693	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73108328	0.83[EUR][1000 genomes]
rs73108346	0.85[EUR][1000 genomes]
rs73999704	0.81[EUR][1000 genomes]
rs73999707	0.85[EUR][1000 genomes]
rs7560000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7578385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7598518	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7601559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7606011	0.93[EUR][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	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv460134	chr2:233639909-233714686	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv584696	chr2:233639909-233714686	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7564410	DGKD	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233565600-233641000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:233585200-233655000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:233611600-233645600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr2:233612000-233640000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:233612000-233644600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr2:233614600-233643600	Weak transcription	Small Intestine	intestine
7	chr2:233620200-233640000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:233621400-233644400	Strong transcription	Liver	Liver
9	chr2:233624400-233640000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:233624800-233640000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:233627800-233645000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:233628600-233644200	Weak transcription	Ovary	ovary
13	chr2:233628600-233655400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:233629200-233655800	Weak transcription	Colonic Mucosa	Colon
15	chr2:233629400-233642000	Weak transcription	Gastric	stomach
16	chr2:233629400-233644200	Weak transcription	Right Ventricle	heart
17	chr2:233629400-233649600	Weak transcription	Spleen	Spleen
18	chr2:233629400-233652600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:233629400-233655200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr2:233629400-233655400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:233630800-233641000	Weak transcription	Fetal Kidney	kidney
22	chr2:233630800-233641200	Weak transcription	Brain Anterior Caudate	brain
23	chr2:233631600-233659200	Weak transcription	Psoas Muscle	Psoas
24	chr2:233632200-233640000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:233633400-233641000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr2:233633400-233652600	Weak transcription	Brain Germinal Matrix	brain
27	chr2:233633600-233649600	Weak transcription	Pancreas	Pancrea
28	chr2:233634000-233640600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:233634000-233641000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:233634000-233643400	Weak transcription	Fetal Heart	heart
31	chr2:233634800-233640000	Strong transcription	HSMM	muscle
32	chr2:233635600-233643200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:233636000-233640800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:233636000-233642000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:233636200-233641000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:233636200-233641000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:233636200-233641200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr2:233636200-233641200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:233636200-233643200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:233636200-233643600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:233636200-233644200	Weak transcription	HMEC	breast
42	chr2:233636200-233646200	Weak transcription	HSMMtube	muscle
43	chr2:233636200-233646400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:233636200-233646400	Weak transcription	K562	blood
45	chr2:233636200-233649600	Weak transcription	Aorta	Aorta
46	chr2:233636200-233649600	Weak transcription	Lung	lung
47	chr2:233636200-233650000	Weak transcription	Fetal Brain Male	brain
48	chr2:233636200-233651400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:233636200-233655200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr2:233636200-233655200	Weak transcription	NHLF	lung

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