Variant report

Variant	rs4560
Chromosome Location	chr7:6063283-6063284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:6049165..6051056-chr7:6063162..6065700,2	K562	blood:
2	chr7:6058638..6061413-chr7:6061770..6064433,3	K562	blood:
3	chr7:6048617..6051234-chr7:6062693..6064451,2	MCF-7	breast:
4	chr7:6062380..6064249-chr7:6070827..6073617,2	MCF-7	breast:
5	chr7:6061286..6063925-chr7:6098268..6100609,3	MCF-7	breast:
6	chr7:6063078..6065231-chr7:6147878..6150172,2	MCF-7	breast:
7	chr7:6062330..6064601-chr7:6141391..6143688,2	MCF-7	breast:
8	chr7:6062377..6067234-chr7:6094768..6099711,6	K562	blood:

Variant related genes	Relation type
ENSG00000252929	Chromatin interaction
ENSG00000122512	Chromatin interaction
ENSG00000157999	Chromatin interaction
ENSG00000086232	Chromatin interaction
ENSG00000106305	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10951972	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10951973	0.82[EUR][1000 genomes]
rs10951974	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11769380	0.80[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12672450	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17136307	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17136342	0.83[LWK][hapmap];0.92[MKK][hapmap];0.86[YRI][hapmap]
rs17343667	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240816	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286681	0.85[ASW][hapmap];0.88[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs2302333	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2302334	0.93[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2345058	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3779106	0.85[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3801030	0.86[LWK][hapmap];0.93[MKK][hapmap];0.93[YRI][hapmap]
rs4724769	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs485254	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs495124	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs551796	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs558030	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]
rs581706	0.93[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62456182	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62456183	0.81[EUR][1000 genomes]
rs62456190	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62456200	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62456202	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs628454	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs629235	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs631491	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs642987	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs646156	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs646160	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs655692	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs661439	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs685415	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs686680	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73331331	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73331344	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs852138	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs852151	0.86[JPT][hapmap]
rs852154	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs865901	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4560	EIF2AK1	cis	parietal	SCAN
rs4560	EIF2AK1	cis	multi-tissue	Pritchard
rs4560	C7orf70	cis	parietal	SCAN
rs4560	EIF2AK1	cis	Lymphoblastoid	GTEx
rs4560	EIF2AK1	cis	normal skin	skin_eQTL
rs4560	EIF2AK1	cis	lymphoblastoid	seeQTL
rs4560	EIF2AK1	cis	cerebellum	SCAN
rs4560	HRI	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	chr7:6050400-6065600	Strong transcription	Lung	lung
4	chr7:6050400-6065800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr7:6050400-6089400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr7:6050400-6095400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr7:6050400-6095600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:6050600-6070000	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr7:6050600-6091000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr7:6050800-6091000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr7:6050800-6095200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:6051000-6095200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr7:6051800-6089600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:6052200-6089400	Strong transcription	Fetal Stomach	stomach
15	chr7:6052600-6094600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr7:6053000-6095000	Strong transcription	Fetal Intestine Small	intestine
17	chr7:6054000-6066000	Strong transcription	Stomach Smooth Muscle	stomach
18	chr7:6054200-6065800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:6054200-6076200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr7:6054400-6063600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:6054400-6068600	Strong transcription	Fetal Brain Female	brain
22	chr7:6054400-6070200	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr7:6054400-6095200	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr7:6054600-6063600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr7:6054600-6063600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:6054600-6063600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:6054600-6063800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr7:6054600-6064000	Strong transcription	HMEC	breast
29	chr7:6054600-6064800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr7:6054600-6064800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:6054600-6065000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr7:6054600-6065200	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr7:6054600-6065200	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr7:6054600-6065400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr7:6054600-6065400	Strong transcription	Primary T cells from cord blood	blood
36	chr7:6054600-6065600	Strong transcription	Left Ventricle	heart
37	chr7:6054600-6065600	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr7:6054600-6066000	Strong transcription	A549	lung
39	chr7:6054600-6066000	Strong transcription	HUVEC	blood vessel
40	chr7:6054600-6067000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr7:6054600-6068400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr7:6054600-6068800	Strong transcription	Hela-S3	cervix
43	chr7:6054600-6090200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr7:6054800-6064400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr7:6054800-6065200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr7:6054800-6065200	Strong transcription	Spleen	Spleen
47	chr7:6054800-6065600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr7:6054800-6075800	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr7:6054800-6089400	Strong transcription	Fetal Intestine Large	intestine
50	chr7:6055200-6064400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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