Variant report

Variant	rs6687899
Chromosome Location	chr1:193029643-193029644
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr1:193027249-193030002	IMR90	lung:	n/a	n/a
2	CREB1	chr1:193027362-193029761	K562	blood:	n/a	n/a
3	MXI1	chr1:193027440-193030657	IMR90	lung:	n/a	n/a
4	REST	chr1:193027452-193029791	H1-neurons	neurons:	n/a	n/a
5	JUN	chr1:193029612-193030350	K562	blood:	n/a	n/a
6	RCOR1	chr1:193027499-193030384	K562	blood:	n/a	n/a
7	MYC	chr1:193029131-193030680	MCF10A-Er-Src	breast:	n/a	n/a
8	TBP	chr1:193028316-193029822	Hela-S3	cervix:	n/a	n/a
9	CHD1	chr1:193027472-193029916	GM12878	blood:	n/a	n/a
10	MAX	chr1:193027478-193029873	Hela-S3	cervix:	n/a	n/a
11	MYC	chr1:193026417-193029763	K562	blood:	n/a	n/a
12	IRF1	chr1:193027422-193030730	K562	blood:	n/a	chr1:193030147-193030160
13	MXI1	chr1:193027245-193030815	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr1:193027428-193029716	PBDE	blood:	n/a	n/a
15	CHD1	chr1:193028664-193029823	H1-hESC	embryonic stem cell:	n/a	n/a
16	MYC	chr1:193027472-193030528	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr1:193027480-193030340	MCF10A-Er-Src	breast:	n/a	n/a
18	GATA1	chr1:193028071-193029951	PBDE	blood:	n/a	n/a
19	EP300	chr1:193029534-193030772	GM12878	blood:	n/a	n/a
20	TBP	chr1:193027232-193029898	K562	blood:	n/a	n/a
21	POLR2A	chr1:193027392-193030696	IMR90	lung:	n/a	n/a
22	POLR2A	chr1:193027316-193030117	MCF10A-Er-Src	breast:	n/a	n/a
23	MXI1	chr1:193027507-193029869	Hela-S3	cervix:	n/a	n/a
24	MAX	chr1:193029635-193030559	NB4	blood:	n/a	n/a
25	POLR2A	chr1:193027390-193030008	Hela-S3	cervix:	n/a	n/a
26	ZNF274	chr1:193029366-193030101	K562	blood:	n/a	n/a
27	HCFC1	chr1:193027155-193030706	Hela-S3	cervix:	n/a	n/a
28	JUN	chr1:193027283-193030901	K562	blood:	n/a	chr1:193028223-193028232
29	IRF1	chr1:193028202-193030706	K562	blood:	n/a	chr1:193030147-193030160
30	UBTF	chr1:193027378-193030494	K562	blood:	n/a	n/a
31	STAT3	chr1:193029625-193029798	MCF10A-Er-Src	breast:	n/a	n/a
32	E2F4	chr1:193028301-193030118	MCF10A-Er-Src	breast:	n/a	chr1:193028448-193028458 chr1:193028557-193028568
33	POLR2A	chr1:193027305-193030001	GM12891	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:192777293..192779700-chr1:193028238..193029983,2	K562	blood:
2	chr1:193025349..193030732-chr1:193089240..193093287,15	MCF-7	breast:
3	chr1:193026932..193030661-chr1:193071909..193075798,10	K562	blood:
4	chr1:192777305..192779700-chr1:193027165..193029983,2	K562	blood:
5	chr1:192993820..193002591-chr1:193021038..193030016,12	K562	blood:
6	chr1:193025655..193031465-chr1:193087281..193093381,17	MCF-7	breast:
7	chr1:193027166..193030257-chr1:193073439..193079424,9	MCF-7	breast:
8	chr1:186341227..186346056-chr1:193025925..193030298,4	K562	blood:
9	chr1:193020543..193046917-chr1:193069266..193098746,125	K562	blood:
10	chr1:193018810..193043703-chr1:193079188..193098601,93	K562	blood:
11	chr1:193027586..193031673-chr1:193072686..193075563,11	MCF-7	breast:

No data

Variant related genes	Relation type
UCHL5	TF binding region
ENSG00000238754	TF binding region
ENSG00000116750	Chromatin interaction
ENSG00000134371	Chromatin interaction
ENSG00000157181	Chromatin interaction
ENSG00000116741	Chromatin interaction
ENSG00000047410	Chromatin interaction
ENSG00000023572	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs16835204	1.00[MEX][hapmap]
rs34552619	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34615282	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55842934	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56199152	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58479385	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6671794	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6682435	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap]
rs6683844	0.91[YRI][hapmap]
rs74130911	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74130912	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74130913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74130914	0.85[AMR][1000 genomes]
rs74130916	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74130917	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74130918	0.85[AMR][1000 genomes]
rs7522932	1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs7553830	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7556154	1.00[MEX][hapmap]
rs7556241	1.00[MEX][hapmap]
rs842806	1.00[MEX][hapmap]
rs842808	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532618	chr1:192537006-193149179	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv998429	chr1:192961698-193050515	Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1002094	chr1:192968080-193084045	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6687899	HBD	trans	lymphoblastoid	seeQTL
rs6687899	CD3D	trans	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:193026600-193029800	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr1:193026600-193030200	Active TSS	K562	blood
3	chr1:193026600-193030800	Active TSS	NHLF	lung
4	chr1:193026800-193030000	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr1:193026800-193030200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr1:193026800-193031000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:193027000-193030000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:193027000-193030000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:193027000-193030000	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr1:193027000-193030000	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr1:193027000-193030000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:193027000-193030000	Active TSS	A549	lung
13	chr1:193027000-193030200	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr1:193027000-193030200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:193027000-193030200	Active TSS	Right Ventricle	heart
16	chr1:193027000-193030800	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr1:193027000-193032600	Active TSS	GM12878-XiMat	blood
18	chr1:193027200-193029800	Active TSS	Fetal Intestine Small	intestine
19	chr1:193027200-193030200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:193027200-193030200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:193027200-193030200	Active TSS	HMEC	breast
22	chr1:193027200-193030600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:193027200-193031000	Active TSS	HSMM	muscle
24	chr1:193027400-193029800	Active TSS	Stomach Mucosa	stomach
25	chr1:193027400-193030000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr1:193027400-193030000	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr1:193027400-193030000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:193027400-193030000	Active TSS	Psoas Muscle	Psoas
29	chr1:193027400-193030200	Active TSS	H9 Cell Line	embryonic stem cell
30	chr1:193027400-193030200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:193027400-193030200	Active TSS	Fetal Intestine Large	intestine
32	chr1:193027400-193030200	Active TSS	Thymus	Thymus
33	chr1:193027400-193030400	Active TSS	Colonic Mucosa	Colon
34	chr1:193027400-193030400	Active TSS	Fetal Muscle Trunk	muscle
35	chr1:193027400-193030600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:193027600-193029800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:193027600-193029800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:193027600-193029800	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr1:193027600-193029800	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr1:193027600-193029800	Active TSS	Osteobl	bone
41	chr1:193027600-193030000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:193027600-193030000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:193027600-193030200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:193027600-193030200	Active TSS	Ovary	ovary
45	chr1:193027600-193030200	Active TSS	Placenta Amnion	Placenta Amnion
46	chr1:193027600-193030200	Active TSS	NHDF-Ad	bronchial
47	chr1:193027800-193029800	Active TSS	Fetal Heart	heart
48	chr1:193027800-193030000	Active TSS	Muscle Satellite Cultured Cells	--
49	chr1:193027800-193030000	Active TSS	Colon Smooth Muscle	Colon
50	chr1:193027800-193030000	Active TSS	Fetal Kidney	kidney

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