Variant report

Variant	rs12538339
Chromosome Location	chr7:6044650-6044651
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	chr7:6041705..6045263-chr7:6045824..6048661,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122512	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12334207	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1805319	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2079819	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2228006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3801032	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3857757	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4720658	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4724768	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4724770	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs475323	0.81[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs523276	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs540208	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6954766	0.84[ASN][1000 genomes]
rs6976251	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7384784	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7803611	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
2	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
3	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
4	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
5	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
6	nsv1034215	chr7:5748982-6056619	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
7	nsv1016690	chr7:5749222-6056619	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
8	nsv1027679	chr7:5760731-6056619	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
10	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
11	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
12	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
13	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
14	nsv433017	chr7:5853557-6045391	Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv830894	chr7:5889658-6072215	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
16	nsv1034916	chr7:5934780-6158970	Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
17	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
18	nsv605998	chr7:6035065-6102034	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
19	nsv1018388	chr7:6038713-6131169	Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
20	nsv970441	chr7:6039097-6048842	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12538339	EIF2AK1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6010400-6048000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:6016200-6047600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr7:6022600-6048000	Weak transcription	NHLF	lung
4	chr7:6025000-6048000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:6025200-6046800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr7:6025800-6045200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr7:6026200-6045400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:6026200-6046200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:6026400-6045000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr7:6026400-6045000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr7:6026400-6045400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr7:6026400-6045600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr7:6026600-6045400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr7:6027600-6047200	Weak transcription	Fetal Kidney	kidney
15	chr7:6028000-6048000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr7:6028200-6045000	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr7:6029000-6048000	Weak transcription	Right Ventricle	heart
18	chr7:6029600-6047000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr7:6032200-6045400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr7:6033600-6045200	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr7:6033600-6045600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr7:6034000-6047600	Weak transcription	Small Intestine	intestine
23	chr7:6035600-6047800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr7:6035600-6048000	Weak transcription	Fetal Heart	heart
25	chr7:6035800-6045200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr7:6035800-6045400	Strong transcription	Fetal Thymus	thymus
27	chr7:6035800-6047000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr7:6035800-6047000	Weak transcription	HepG2	liver
29	chr7:6035800-6047600	Weak transcription	HSMMtube	muscle
30	chr7:6035800-6047800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr7:6035800-6047800	Weak transcription	NH-A	brain
32	chr7:6035800-6048000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr7:6035800-6048000	Weak transcription	Pancreas	Pancrea
34	chr7:6035800-6048000	Weak transcription	Psoas Muscle	Psoas
35	chr7:6036000-6045200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr7:6036000-6047600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr7:6036000-6047600	Weak transcription	HMEC	breast
38	chr7:6036000-6048000	Weak transcription	Fetal Brain Male	brain
39	chr7:6036600-6047000	Weak transcription	NHEK	skin
40	chr7:6037400-6047400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr7:6037600-6045400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr7:6039000-6048000	Weak transcription	Colon Smooth Muscle	Colon
43	chr7:6039200-6046400	Weak transcription	K562	blood
44	chr7:6039200-6048000	Weak transcription	NHDF-Ad	bronchial
45	chr7:6039400-6047600	Weak transcription	Fetal Lung	lung
46	chr7:6039800-6047000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr7:6039800-6047600	Weak transcription	HSMM	muscle
48	chr7:6039800-6048000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr7:6039800-6048000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr7:6040000-6047000	Weak transcription	Primary B cells from cord blood	blood

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