Variant report

Variant	rs475323
Chromosome Location	chr7:6090600-6090601
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MBD4	chr7:6090428-6090921	HepG2	liver:	n/a	n/a
2	FOXA1	chr7:6090363-6090841	HepG2	liver:	n/a	chr7:6090626-6090641
3	FOSL2	chr7:6090405-6090745	A549	lung:	n/a	n/a
4	FOXA2	chr7:6090421-6090759	A549	lung:	n/a	n/a
5	RXRA	chr7:6090544-6090866	HepG2	liver:	n/a	n/a
6	FOSL2	chr7:6090320-6090780	HepG2	liver:	n/a	n/a
7	FOXA2	chr7:6090301-6090737	A549	lung:	n/a	n/a
8	EP300	chr7:6090416-6090974	HepG2	liver:	n/a	n/a
9	FOXA1	chr7:6090361-6090814	T-47D	breast:	n/a	chr7:6090626-6090641
10	EP300	chr7:6090368-6090999	HepG2	liver:	n/a	n/a
11	FOXA1	chr7:6090258-6091018	HepG2	liver:	n/a	chr7:6090626-6090641
12	JUND	chr7:6090406-6090765	HepG2	liver:	n/a	n/a
13	FOXA2	chr7:6090453-6090881	HepG2	liver:	n/a	n/a
14	RAD21	chr7:6090518-6090847	HepG2	liver:	n/a	n/a
15	RCOR1	chr7:6090500-6090803	HepG2	liver:	n/a	n/a
16	TBP	chr7:6090413-6090861	HepG2	liver:	n/a	n/a
17	MXI1	chr7:6090468-6090927	HepG2	liver:	n/a	n/a
18	NFIC	chr7:6090357-6090999	HepG2	liver:	n/a	n/a
19	SP1	chr7:6090363-6090871	HepG2	liver:	n/a	n/a
20	FOSL2	chr7:6090361-6090846	HepG2	liver:	n/a	n/a
21	HDAC2	chr7:6090381-6090955	HepG2	liver:	n/a	n/a
22	FOXA1	chr7:6090266-6091017	HepG2	liver:	n/a	chr7:6090626-6090641
23	HDAC2	chr7:6090452-6090808	HepG2	liver:	n/a	n/a
24	POLR2A	chr7:6090456-6090802	HepG2	liver:	n/a	n/a
25	MAX	chr7:6090450-6090949	HepG2	liver:	n/a	n/a
26	JUND	chr7:6090398-6090966	HepG2	liver:	n/a	n/a
27	JUN	chr7:6090458-6090849	HepG2	liver:	n/a	n/a
28	MYBL2	chr7:6090269-6091272	HepG2	liver:	n/a	n/a
29	FOXA1	chr7:6090472-6090760	T-47D	breast:	n/a	chr7:6090626-6090641
30	ARID3A	chr7:6090500-6091007	HepG2	liver:	n/a	n/a
31	POLR2A	chr7:6090526-6091013	K562	blood:	n/a	n/a
32	TEAD4	chr7:6090364-6091011	HepG2	liver:	n/a	chr7:6090647-6090656
33	NFIC	chr7:6090483-6090877	HepG2	liver:	n/a	n/a
34	FOXA1	chr7:6090256-6091010	HepG2	liver:	n/a	chr7:6090626-6090641
35	MYBL2	chr7:6090400-6090939	HepG2	liver:	n/a	n/a
36	FOXA2	chr7:6090099-6091007	HepG2	liver:	n/a	n/a
37	SMC3	chr7:6090503-6090847	HepG2	liver:	n/a	n/a
38	BHLHE40	chr7:6090476-6090889	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:6088385..6094531-chr7:6095693..6100506,11	MCF-7	breast:
2	chr7:6089956..6092329-chr7:6093518..6095916,2	K562	blood:
3	chr7:6084536..6086826-chr7:6088354..6091112,2	K562	blood:
4	chr7:6090422..6101465-chr7:6116449..6124326,16	K562	blood:
5	chr7:6084454..6086728-chr7:6090555..6092225,2	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANKRD61-1	chr7:6090586-6090829	NONHSAT118969
2	lnc-ANKRD61-1	chr7:6090586-6090829	NONHSAT118968
3	lnc-ANKRD61-1	chr7:6090586-6090829	NONHSAT118971

No data

Variant related genes	Relation type
EIF2AK1	TF binding region
RN7SL851P	TF binding region
ENSG00000231704	Chromatin interaction
ENSG00000264605	Chromatin interaction
ENSG00000252929	Chromatin interaction
ENSG00000086232	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10263017	0.85[ASW][hapmap]
rs11766581	0.92[ASW][hapmap]
rs12334207	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12538339	0.81[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1805319	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2079819	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2228006	0.88[MEX][hapmap];0.83[AMR][1000 genomes]
rs3801032	0.92[ASW][hapmap];0.87[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3857757	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4720658	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4724768	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4724770	0.93[CEU][hapmap];0.85[CHB][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs523276	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs525090	0.85[ASW][hapmap]
rs540208	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs569173	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs601199	0.81[AMR][1000 genomes]
rs6463527	0.85[ASW][hapmap]
rs6976251	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7384784	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7803611	0.93[CEU][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs475323	EIF2AK1	Cis_1M	lymphoblastoid	RTeQTL
rs475323	EIF3B	cis	cerebellum	SCAN

Chromatin state (count:138 , 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	chr7:6050400-6095400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:6050400-6095600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:6050600-6091000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr7:6050800-6091000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr7:6050800-6095200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:6051000-6095200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr7:6052600-6094600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:6053000-6095000	Strong transcription	Fetal Intestine Small	intestine
11	chr7:6054400-6095200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr7:6056400-6095200	Strong transcription	Dnd41	blood
13	chr7:6056600-6095200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:6056800-6090600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr7:6056800-6094800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:6066600-6094600	Strong transcription	Fetal Muscle Leg	muscle
17	chr7:6066800-6091200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr7:6066800-6094800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:6066800-6095200	Strong transcription	Fetal Thymus	thymus
20	chr7:6067000-6094600	Strong transcription	Placenta	Placenta
21	chr7:6067800-6095200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr7:6068000-6094400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr7:6071000-6094600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr7:6071200-6090600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr7:6071600-6097200	Weak transcription	Right Atrium	heart
26	chr7:6072600-6095000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:6073000-6090800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr7:6076000-6097800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr7:6080000-6092800	Strong transcription	Primary T cells from cord blood	blood
30	chr7:6083000-6090600	Weak transcription	Stomach Mucosa	stomach
31	chr7:6083200-6097400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr7:6083600-6097200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr7:6084400-6093600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr7:6084400-6096400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr7:6084400-6098200	Weak transcription	Esophagus	oesophagus
36	chr7:6084600-6093800	Weak transcription	NHLF	lung
37	chr7:6085000-6094000	Weak transcription	Aorta	Aorta
38	chr7:6085000-6096600	Weak transcription	HUVEC	blood vessel
39	chr7:6085200-6095000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr7:6085200-6097200	Weak transcription	Psoas Muscle	Psoas
41	chr7:6085400-6093800	Weak transcription	NHEK	skin
42	chr7:6085400-6097000	Weak transcription	Colon Smooth Muscle	Colon
43	chr7:6086000-6093600	Weak transcription	Spleen	Spleen
44	chr7:6086000-6098200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:6086200-6097000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr7:6086400-6096400	Weak transcription	NHDF-Ad	bronchial
47	chr7:6086800-6097600	Weak transcription	Fetal Kidney	kidney
48	chr7:6087000-6096600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr7:6087200-6092200	Strong transcription	K562	blood
50	chr7:6087600-6097000	Weak transcription	HSMMtube	muscle

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