Variant report

Variant	rs558030
Chromosome Location	chr7:6097667-6097668
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:6082731..6088079-chr7:6097012..6099885,4	MCF-7	breast:
2	chr7:6094946..6099638-chr7:6140891..6146239,12	K562	blood:
3	chr7:6047262..6048916-chr7:6096593..6098744,2	MCF-7	breast:
4	chr7:6064770..6067105-chr7:6097512..6099982,2	K562	blood:
5	chr7:6096872..6099965-chr7:6142845..6147736,5	MCF-7	breast:
6	chr7:6096078..6098948-chr7:6116857..6121575,6	K562	blood:
7	chr7:6095667..6100309-chr7:6118978..6123029,12	MCF-7	breast:
8	chr7:6062377..6067234-chr7:6094768..6099711,6	K562	blood:
9	chr7:5631641..5634228-chr7:6097200..6099216,2	K562	blood:
10	chr7:6055912..6057708-chr7:6097324..6099828,2	MCF-7	breast:
11	chr7:6096763..6100631-chr7:6141376..6146373,15	MCF-7	breast:
12	chr7:6097184..6100296-chr7:6118283..6122245,9	MCF-7	breast:
13	chr7:6047579..6050679-chr7:6097211..6100186,3	MCF-7	breast:
14	chr7:6094497..6101614-chr7:6140891..6145784,14	K562	blood:
15	chr7:6047930..6051239-chr7:6095534..6098918,6	K562	blood:
16	chr7:6048500..6051239-chr7:6096959..6099959,3	K562	blood:
17	chr7:6097568..6100190-chr7:6387069..6389785,3	MCF-7	breast:
18	chr7:6090422..6101465-chr7:6116449..6124326,16	K562	blood:

No data

Variant related genes	Relation type
ENSG00000122512	Chromatin interaction
ENSG00000106305	Chromatin interaction
ENSG00000207217	Chromatin interaction
ENSG00000231704	Chromatin interaction
ENSG00000264605	Chromatin interaction
ENSG00000106346	Chromatin interaction
ENSG00000240718	Chromatin interaction
ENSG00000086232	Chromatin interaction
ENSG00000178397	Chromatin interaction
ENSG00000075618	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10951974	0.86[EUR][1000 genomes]
rs11769380	0.91[CEU][hapmap]
rs12672450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17136307	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17343667	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2240816	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2286681	0.96[CEU][hapmap]
rs2302333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2302334	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3779106	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs3801030	0.86[YRI][hapmap]
rs4560	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4724769	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs485254	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs495124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs551796	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs581706	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62456190	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62456200	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62456202	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs628454	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs629235	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs631491	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs642987	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs646156	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs646160	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs655692	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs661439	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs685415	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs686680	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73331344	0.86[EUR][1000 genomes]
rs852138	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs852151	0.86[JPT][hapmap]
rs852154	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs865901	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv1021037	chr7:6070792-6426966	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
15	nsv538713	chr7:6070792-6426966	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
16	esv3405881	chr7:6087760-6122016	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs558030	HRI	cis	multi-tissue	Pritchard
rs558030	EIF2AK1	cis	lesional skin	skin_eQTL
rs558030	EIF2AK1	Cis_1M	lymphoblastoid	RTeQTL
rs558030	EIF2AK1	cis	normal skin	skin_eQTL
rs558030	EIF2AK1	cis	Lymphoblastoid	GTEx
rs558030	EIF2AK1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6049400-6098000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:6050000-6097800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:6076000-6097800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:6084400-6098200	Weak transcription	Esophagus	oesophagus
5	chr7:6086000-6098200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:6089400-6097800	Weak transcription	Left Ventricle	heart
7	chr7:6095400-6099400	Active TSS	K562	blood
8	chr7:6095600-6097800	Weak transcription	Pancreas	Pancrea
9	chr7:6096000-6097800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:6096400-6097800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:6096400-6097800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:6096400-6097800	Enhancers	Primary T cells fromperipheralblood	blood
13	chr7:6096400-6097800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr7:6096400-6097800	Flanking Active TSS	Hela-S3	cervix
15	chr7:6096400-6099200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr7:6096400-6099200	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr7:6096600-6097800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:6096600-6097800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr7:6096600-6097800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:6096600-6097800	Enhancers	Fetal Thymus	thymus
21	chr7:6096600-6097800	Flanking Active TSS	GM12878-XiMat	blood
22	chr7:6096600-6098000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr7:6096600-6098000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr7:6096600-6098000	Active TSS	HepG2	liver
25	chr7:6096600-6098400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:6096800-6098000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr7:6096800-6099000	Active TSS	HMEC	breast
28	chr7:6096800-6099400	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr7:6096800-6099400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr7:6097000-6097800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr7:6097000-6097800	Enhancers	Brain Angular Gyrus	brain
32	chr7:6097000-6097800	Enhancers	Fetal Lung	lung
33	chr7:6097000-6097800	Enhancers	Fetal Muscle Leg	muscle
34	chr7:6097000-6097800	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr7:6097000-6097800	Flanking Active TSS	Osteobl	bone
36	chr7:6097000-6098000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr7:6097000-6098000	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr7:6097000-6098000	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr7:6097000-6098000	Enhancers	Primary B cells from peripheral blood	blood
40	chr7:6097000-6098000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr7:6097000-6098000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr7:6097000-6098000	Enhancers	Colon Smooth Muscle	Colon
43	chr7:6097000-6098000	Enhancers	Fetal Brain Male	brain
44	chr7:6097000-6098000	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr7:6097000-6098200	Flanking Active TSS	NH-A	brain
46	chr7:6097000-6098600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr7:6097000-6098600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr7:6097000-6098600	Flanking Active TSS	Brain Germinal Matrix	brain
49	chr7:6097000-6099000	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr7:6097000-6099200	Active TSS	Placenta	Placenta

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