Variant report

Variant	rs61828539
Chromosome Location	chr1:212211476-212211477
allele	A/G
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	POLR2A	chr1:212211307-212211495	H1-hESC	embryonic stem cell:	n/a	n/a
2	MYC	chr1:212211278-212211611	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:212211343-212211503	GM12878	blood:	n/a	n/a
4	MAX	chr1:212211246-212211546	K562	blood:	n/a	n/a
5	STAT3	chr1:212211283-212211551	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:212211291-212211793	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr1:212211328-212211522	GM12878	blood:	n/a	n/a
8	CEBPB	chr1:212211280-212211564	Hela-S3	cervix:	n/a	chr1:212211396-212211407
9	FOS	chr1:212211229-212211634	MCF10A-Er-Src	breast:	n/a	n/a
10	MYC	chr1:212211379-212211490	NB4	blood:	n/a	n/a
11	POLR2A	chr1:212211234-212211593	GM12878	blood:	n/a	n/a
12	FOS	chr1:212211246-212211607	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr1:212211278-212211567	MCF10A-Er-Src	breast:	n/a	n/a
14	WRNIP1	chr1:212211063-212211744	GM12878	blood:	n/a	n/a
15	EBF1	chr1:212211292-212211629	GM12878	blood:	n/a	n/a
16	CEBPB	chr1:212211293-212211548	HepG2	liver:	n/a	chr1:212211396-212211407
17	STAT3	chr1:212211309-212211515	MCF10A-Er-Src	breast:	n/a	n/a
18	STAT3	chr1:212211298-212211512	MCF10A-Er-Src	breast:	n/a	n/a
19	CEBPB	chr1:212211308-212211560	K562	blood:	n/a	chr1:212211396-212211407
20	HEY1	chr1:212211214-212211570	K562	blood:	n/a	n/a
21	TBP	chr1:212211414-212211619	GM12878	blood:	n/a	n/a
22	MAX	chr1:212211335-212211575	NB4	blood:	n/a	n/a
23	POLR2A	chr1:212211183-212211477	K562	blood:	n/a	n/a
24	POLR2A	chr1:212211217-212211741	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr1:212211345-212211476	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr1:212211267-212211517	Hela-S3	cervix:	n/a	n/a
27	MXI1	chr1:212211348-212211478	GM12878	blood:	n/a	n/a
28	FOS	chr1:212211286-212211585	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr1:212210881-212211756	H1-hESC	embryonic stem cell:	n/a	n/a
30	MYC	chr1:212211166-212211815	MCF10A-Er-Src	breast:	n/a	n/a
31	E2F4	chr1:212211314-212211728	MCF10A-Er-Src	breast:	n/a	n/a
32	STAT1	chr1:212211371-212211519	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212207393..212212126-chr1:212456103..212460187,5	K562	blood:

Variant related genes	Relation type
INTS7	TF binding region
ENSG00000066027	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10863936	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11119836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119843	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12066042	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12070369	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12076757	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12089230	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1387814	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1387815	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17656163	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17656362	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17656453	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17699790	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17700264	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2358333	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4093392	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4394721	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951560	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4951561	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4951567	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55806741	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55960291	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56289586	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56292525	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61828530	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61828533	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61828543	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61828547	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61830761	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6657728	0.83[AFR][1000 genomes]
rs6675660	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs66858610	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67417805	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519826	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7525895	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7540968	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61828539	INTS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212209200-212212000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:212209400-212217800	Weak transcription	Small Intestine	intestine
3	chr1:212209600-212226600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:212209600-212253000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:212209800-212211600	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr1:212209800-212214000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:212210200-212212000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:212210200-212213800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:212210200-212214000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:212210400-212211600	Enhancers	Fetal Lung	lung
11	chr1:212210400-212211600	Flanking Active TSS	HepG2	liver
12	chr1:212210400-212214000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:212210400-212214000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:212210400-212214000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:212210400-212223600	Weak transcription	HSMM	muscle
16	chr1:212210400-212227400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr1:212210400-212228800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:212210400-212228800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:212210400-212228800	Weak transcription	Fetal Intestine Large	intestine
20	chr1:212210600-212211600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:212210600-212211800	Enhancers	Primary hematopoietic stem cells	blood
22	chr1:212210600-212212400	Transcr. at gene 5' and 3'	K562	blood
23	chr1:212210600-212213800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr1:212210600-212213800	Weak transcription	Primary T cells from cord blood	blood
25	chr1:212210600-212214000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:212210600-212214000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:212210600-212214600	Transcr. at gene 5' and 3'	Dnd41	blood
28	chr1:212210600-212215600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:212210600-212227400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:212210600-212229200	Weak transcription	Fetal Brain Female	brain
31	chr1:212210800-212211600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:212210800-212211600	Active TSS	Fetal Brain Male	brain
33	chr1:212210800-212211600	Weak transcription	Fetal Heart	heart
34	chr1:212210800-212211600	Enhancers	NHDF-Ad	bronchial
35	chr1:212210800-212211800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:212210800-212211800	Weak transcription	Fetal Kidney	kidney
37	chr1:212210800-212212000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
38	chr1:212210800-212212000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:212210800-212212000	Active TSS	Brain Germinal Matrix	brain
40	chr1:212210800-212213800	Weak transcription	Thymus	Thymus
41	chr1:212210800-212214000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:212210800-212214000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:212210800-212216800	Weak transcription	Fetal Intestine Small	intestine
44	chr1:212210800-212217400	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:212210800-212220800	Weak transcription	Fetal Stomach	stomach
46	chr1:212210800-212241200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr1:212211000-212211600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:212211000-212211600	Flanking Active TSS	GM12878-XiMat	blood
49	chr1:212211000-212211600	Enhancers	NHEK	skin
50	chr1:212211000-212211800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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