Variant report

Variant	rs2640
Chromosome Location	chr7:6066450-6066451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr7:6065998-6066494	K562	blood:	n/a	chr7:6066261-6066274
2	SPI1	chr7:6066406-6066818	GM12891	blood:	n/a	chr7:6066605-6066618 chr7:6066608-6066617
3	SPI1	chr7:6066084-6066898	GM12878	blood:	n/a	chr7:6066605-6066618 chr7:6066608-6066617
4	ELF1	chr7:6065934-6066561	MCF-7	breast:	n/a	n/a
5	CTCF	chr7:6066380-6066530	WI-38	lung:	n/a	n/a
6	POLR2A	chr7:6065541-6066466	Hela-S3	cervix:	n/a	n/a
7	RAD21	chr7:6066142-6066526	A549	lung:	n/a	n/a
8	RAD21	chr7:6066023-6066513	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr7:6065920-6066540	HL-60	blood:	n/a	n/a
10	RAD21	chr7:6066086-6066475	H1-hESC	embryonic stem cell:	n/a	n/a
11	ZNF384	chr7:6066449-6066506	GM12878	blood:	n/a	n/a
12	POLR2A	chr7:6065665-6066512	GM18505	blood:	n/a	n/a
13	ELF1	chr7:6066061-6066467	K562	blood:	n/a	n/a
14	USF2	chr7:6066169-6066511	Hela-S3	cervix:	n/a	n/a
15	UBTF	chr7:6066191-6066576	K562	blood:	n/a	n/a
16	RAD21	chr7:6065958-6066637	HCT-116	colon:	n/a	n/a
17	ZC3H11A	chr7:6066369-6066484	K562	blood:	n/a	n/a
18	EP300	chr7:6066317-6066543	K562	blood:	n/a	n/a
19	SPI1	chr7:6066072-6066962	HL-60	blood:	n/a	chr7:6066605-6066618 chr7:6066608-6066617
20	BHLHE40	chr7:6065932-6066839	GM12878	blood:	n/a	n/a
21	SMC3	chr7:6066177-6066455	K562	blood:	n/a	n/a
22	CTCF	chr7:6066300-6066450	HFF-Myc	foreskin:	n/a	n/a
23	TBL1XR1	chr7:6065840-6066549	GM12878	blood:	n/a	n/a
24	RAD21	chr7:6066028-6066484	HepG2	liver:	n/a	n/a
25	CTCF	chr7:6065927-6066637	A549	lung:	n/a	chr7:6066261-6066274 chr7:6065930-6065943
26	CTCF	chr7:6066106-6066458	K562	blood:	n/a	chr7:6066261-6066274
27	RAD21	chr7:6066119-6066559	MCF-7	breast:	n/a	n/a
28	POLR2A	chr7:6066132-6066485	HepG2	liver:	n/a	n/a
29	CUX1	chr7:6066449-6066535	K562	blood:	n/a	n/a
30	CTCF	chr7:6066360-6066510	NHLF	lung:	n/a	n/a
31	EBF1	chr7:6065635-6066954	GM12878	blood:	n/a	n/a
32	POLR2A	chr7:6059503-6066475	PANC-1	pancreas:	n/a	n/a
33	RAD21	chr7:6066115-6066476	Hela-S3	cervix:	n/a	n/a
34	CHD1	chr7:6066298-6066491	GM12878	blood:	n/a	n/a
35	CTCF	chr7:6066081-6066463	GM12878	blood:	n/a	chr7:6066261-6066274
36	IKZF1	chr7:6066392-6066589	GM12878	blood:	n/a	n/a
37	CTCF	chr7:6066084-6066482	H1-hESC	embryonic stem cell:	n/a	chr7:6066261-6066274
38	RAD21	chr7:6066064-6066472	SK-N-SH_RA	brain:	n/a	n/a
39	RAD21	chr7:6066102-6066487	HepG2	liver:	n/a	n/a
40	RAD21	chr7:6066065-6066528	HCT-116	colon:	n/a	n/a
41	RCOR1	chr7:6066149-6066919	GM12878	blood:	n/a	n/a
42	POLR2A	chr7:6066167-6066474	HCT-116	colon:	n/a	n/a
43	POLR2A	chr7:6065698-6066474	GM12892	blood:	n/a	n/a
44	SMC3	chr7:6066072-6066454	Hela-S3	cervix:	n/a	n/a
45	SMC3	chr7:6066172-6066473	HepG2	liver:	n/a	n/a
46	POLR2A	chr7:6064936-6067718	K562	blood:	n/a	n/a
47	POLR2A	chr7:6066433-6066522	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6066319..6068203-chr7:6069919..6071958,2	MCF-7	breast:
2	chr7:6065831..6068709-chr7:6141820..6144838,4	MCF-7	breast:
3	chr7:6064661..6068184-chr7:6142795..6145849,5	MCF-7	breast:
4	chr7:6064418..6067500-chr7:6069656..6072436,4	MCF-7	breast:
5	chr7:6047363..6049354-chr7:6063912..6067391,3	MCF-7	breast:
6	chr7:6064770..6067105-chr7:6097512..6099982,2	K562	blood:
7	chr7:6063761..6069877-chr7:6069933..6073533,9	K562	blood:
8	chr7:6055942..6058013-chr7:6065657..6067838,2	MCF-7	breast:
9	chr7:6062377..6067234-chr7:6094768..6099711,6	K562	blood:

Variant related genes	Relation type
EIF2AK1	TF binding region
ANKRD61	TF binding region
ENSG00000106305	Chromatin interaction
ENSG00000207217	Chromatin interaction
ENSG00000157999	Chromatin interaction
ENSG00000106346	Chromatin interaction
ENSG00000252929	Chromatin interaction
ENSG00000086232	Chromatin interaction
ENSG00000122512	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10447573	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12154418	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12155022	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12532865	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17136324	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17136348	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2302329	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3213665	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35058104	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41282676	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57846353	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61227749	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7803143	1.00[CEU][hapmap];1.00[LWK][hapmap];0.85[TSI][hapmap]
rs9639021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9640011	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9640013	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9640014	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2640	EIF2AK1	cis	lymphoblastoid	seeQTL

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	chr7:6050400-6089400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr7:6050400-6095400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:6050400-6095600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:6050600-6070000	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr7:6050600-6091000	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr7:6050800-6091000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr7:6050800-6095200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr7:6051000-6095200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr7:6051800-6089600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:6052200-6089400	Strong transcription	Fetal Stomach	stomach
13	chr7:6052600-6094600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:6053000-6095000	Strong transcription	Fetal Intestine Small	intestine
15	chr7:6054200-6076200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:6054400-6068600	Strong transcription	Fetal Brain Female	brain
17	chr7:6054400-6070200	Strong transcription	H9 Cell Line	embryonic stem cell
18	chr7:6054400-6095200	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr7:6054600-6067000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr7:6054600-6068400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr7:6054600-6068800	Strong transcription	Hela-S3	cervix
22	chr7:6054600-6090200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr7:6054800-6075800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr7:6054800-6089400	Strong transcription	Fetal Intestine Large	intestine
25	chr7:6055800-6068800	Strong transcription	Fetal Lung	lung
26	chr7:6055800-6069800	Strong transcription	Brain Hippocampus Middle	brain
27	chr7:6055800-6081000	Strong transcription	HepG2	liver
28	chr7:6055800-6089000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr7:6056000-6068600	Strong transcription	Brain Substantia Nigra	brain
30	chr7:6056000-6089600	Strong transcription	Liver	Liver
31	chr7:6056200-6067600	Strong transcription	NHEK	skin
32	chr7:6056400-6073000	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr7:6056400-6085400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr7:6056400-6095200	Strong transcription	Dnd41	blood
35	chr7:6056600-6067800	Strong transcription	HSMMtube	muscle
36	chr7:6056600-6095200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:6056800-6067000	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr7:6056800-6089400	Strong transcription	Osteobl	bone
39	chr7:6056800-6090000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr7:6056800-6090600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr7:6056800-6094800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr7:6059400-6068600	Strong transcription	Brain Anterior Caudate	brain
43	chr7:6059600-6068600	Strong transcription	NHLF	lung
44	chr7:6059600-6070400	Strong transcription	Brain Germinal Matrix	brain
45	chr7:6060000-6069400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr7:6060200-6067000	Strong transcription	Pancreas	Pancrea
47	chr7:6060200-6076000	Strong transcription	Gastric	stomach
48	chr7:6060400-6068600	Strong transcription	Fetal Kidney	kidney
49	chr7:6060400-6070000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr7:6060600-6068600	Strong transcription	Placenta Amnion	Placenta Amnion

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