Variant report

Variant	rs1860459
Chromosome Location	chr7:6056619-6056620
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:6055602..6058271-chr7:6142750..6144893,2	MCF-7	breast:
2	chr7:6054308..6057610-chr7:6144384..6145966,3	K562	blood:
3	chr7:6055942..6058013-chr7:6065657..6067838,2	MCF-7	breast:
4	chr7:6055912..6057708-chr7:6097324..6099828,2	MCF-7	breast:
5	chr7:6046629..6049121-chr7:6054916..6059212,5	K562	blood:
6	chr7:6055317..6057272-chr7:6144133..6145966,2	K562	blood:

Variant related genes	Relation type
ENSG00000106346	Chromatin interaction
ENSG00000086232	Chromatin interaction
ENSG00000122512	Chromatin interaction
ENSG00000106305	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10249956	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12333405	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12334093	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2024002	0.93[CEU][hapmap]
rs2906502	1.00[CEU][hapmap]
rs2952939	0.94[CEU][hapmap]
rs3094962	0.94[CEU][hapmap]
rs41280717	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55839766	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs56000981	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56223935	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56354402	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59790240	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73056639	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73056648	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73056662	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
15	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
16	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
17	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
18	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1860459	EIF2AK1	cis	cerebellum	SCAN
rs1860459	EIF2AK1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6049200-6061800	Weak transcription	Fetal Brain Male	brain
2	chr7:6049400-6061400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr7:6049400-6098000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr7:6049600-6060400	Weak transcription	Fetal Kidney	kidney
5	chr7:6049600-6060600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:6050000-6057200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:6050000-6097800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:6050400-6065600	Strong transcription	Lung	lung
9	chr7:6050400-6065800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr7:6050400-6089400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr7:6050400-6095400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:6050400-6095600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:6050600-6057600	Strong transcription	Primary hematopoietic stem cells	blood
14	chr7:6050600-6070000	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr7:6050600-6091000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr7:6050800-6062000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr7:6050800-6091000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr7:6050800-6095200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr7:6051000-6062200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr7:6051000-6095200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr7:6051800-6089600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:6052200-6089400	Strong transcription	Fetal Stomach	stomach
23	chr7:6052400-6062000	Weak transcription	Small Intestine	intestine
24	chr7:6052600-6094600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr7:6053000-6095000	Strong transcription	Fetal Intestine Small	intestine
26	chr7:6054000-6066000	Strong transcription	Stomach Smooth Muscle	stomach
27	chr7:6054200-6065800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:6054200-6076200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr7:6054400-6063600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr7:6054400-6068600	Strong transcription	Fetal Brain Female	brain
31	chr7:6054400-6070200	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr7:6054400-6095200	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr7:6054600-6056800	Genic enhancers	Muscle Satellite Cultured Cells	--
34	chr7:6054600-6057200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr7:6054600-6057800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr7:6054600-6058000	Strong transcription	Brain Germinal Matrix	brain
37	chr7:6054600-6059200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr7:6054600-6059400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr7:6054600-6063000	Strong transcription	Duodenum Mucosa	Duodenum
40	chr7:6054600-6063600	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr7:6054600-6063600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr7:6054600-6063600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr7:6054600-6063800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr7:6054600-6064000	Strong transcription	HMEC	breast
45	chr7:6054600-6064800	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr7:6054600-6064800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr7:6054600-6065000	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr7:6054600-6065200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr7:6054600-6065200	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr7:6054600-6065400	Strong transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links