Variant report

Variant	rs1857909
Chromosome Location	chr11:18548881-18548882
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	JUN	chr11:18547649-18548948	K562	blood:	n/a	chr11:18548088-18548102
2	SPI1	chr11:18548116-18548914	HL-60	blood:	n/a	chr11:18548493-18548502 chr11:18548468-18548477 chr11:18548491-18548504
3	MXI1	chr11:18547900-18549507	Hela-S3	cervix:	n/a	n/a
4	GABPA	chr11:18547791-18549043	MCF-7	breast:	n/a	chr11:18548495-18548502
5	POLR2A	chr11:18547891-18549011	H1-neurons	neurons:	n/a	n/a
6	CHD2	chr11:18547904-18548939	GM12878	blood:	n/a	n/a
7	CHD2	chr11:18547887-18548913	Hela-S3	cervix:	n/a	n/a
8	MYC	chr11:18547850-18548928	K562	blood:	n/a	chr11:18548119-18548129
9	POLR2A	chr11:18547893-18548891	HepG2	liver:	n/a	n/a
10	MXI1	chr11:18547960-18549193	GM12878	blood:	n/a	n/a
11	EBF1	chr11:18548306-18548935	GM12878	blood:	n/a	n/a
12	POLR2A	chr11:18547944-18548897	GM12878	blood:	n/a	n/a
13	MXI1	chr11:18547915-18548976	HepG2	liver:	n/a	n/a
14	MAX	chr11:18547870-18548949	A549	lung:	n/a	chr11:18548119-18548129
15	BHLHE40	chr11:18548135-18548907	K562	blood:	n/a	n/a
16	RELA	chr11:18547791-18548902	GM19099	blood:	n/a	n/a
17	MAZ	chr11:18547998-18548881	Hela-S3	cervix:	n/a	chr11:18548119-18548129
18	MAX	chr11:18547836-18548946	ECC-1	luminal epithelium:	n/a	chr11:18548119-18548129
19	HA-E2F1	chr11:18547898-18548940	MCF-7	breast:	n/a	chr11:18548284-18548298 chr11:18548265-18548280
20	POLR2A	chr11:18547906-18548925	U87	brain:	n/a	n/a
21	SIN3AK20	chr11:18547623-18549044	MCF-7	breast:	n/a	n/a
22	ELF1	chr11:18547750-18549018	HCT-116	colon:	n/a	chr11:18548513-18548522 chr11:18548466-18548477 chr11:18548465-18548478 chr11:18548493-18548502 chr11:18548512-18548523
23	GABPA	chr11:18547954-18548910	K562	blood:	n/a	chr11:18548495-18548502
24	SMARCB1	chr11:18547905-18548943	Hela-S3	cervix:	n/a	n/a
25	SMC3	chr11:18547765-18549516	Hela-S3	cervix:	n/a	chr11:18548287-18548297
26	TAF1	chr11:18547959-18548914	H1-neurons	neurons:	n/a	n/a
27	TBL1XR1	chr11:18548154-18549155	K562	blood:	n/a	n/a
28	POLR2A	chr11:18547776-18548977	Hela-S3	cervix:	n/a	n/a
29	HEY1	chr11:18547864-18548976	HepG2	liver:	n/a	n/a
30	CCNT2	chr11:18548046-18548906	K562	blood:	n/a	n/a
31	POLR2A	chr11:18547868-18548881	GM18526	blood:	n/a	n/a
32	POLR2A	chr11:18547452-18549568	HUVEC	blood vessel:	n/a	n/a
33	GTF2B	chr11:18548330-18548909	K562	blood:	n/a	n/a
34	HEY1	chr11:18547810-18548973	HepG2	liver:	n/a	n/a
35	POLR2A	chr11:18547865-18548927	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr11:18547828-18548925	U87	brain:	n/a	n/a
37	POLR2A	chr11:18547840-18549190	PFSK-1	brain:	n/a	n/a
38	YY1	chr11:18547970-18548895	GM12878	blood:	n/a	chr11:18548413-18548424 chr11:18548280-18548294
39	POLR2A	chr11:18547901-18549385	K562	blood:	n/a	n/a
40	EBF1	chr11:18548012-18548889	GM12878	blood:	n/a	n/a
41	CREB1	chr11:18547890-18548920	GM12878	blood:	n/a	n/a
42	SPI1	chr11:18548127-18548894	GM12878	blood:	n/a	chr11:18548493-18548502 chr11:18548468-18548477 chr11:18548491-18548504
43	IRF1	chr11:18547686-18549013	K562	blood:	n/a	chr11:18547868-18547878 chr11:18547867-18547879
44	MYC	chr11:18548012-18548998	K562	blood:	n/a	chr11:18548119-18548129
45	POLR2A	chr11:18547962-18548906	MCF-7	breast:	n/a	n/a
46	TBP	chr11:18547853-18549008	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr11:18547890-18549135	Raji	blood:	n/a	n/a
48	CEBPB	chr11:18547782-18549468	A549	lung:	n/a	chr11:18549188-18549199
49	POLR2A	chr11:18547906-18549610	K562	blood:	n/a	n/a
50	POLR2A	chr11:18547909-18549216	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:18546372..18549758-chr11:18653531..18658575,7	K562	blood:
2	chr11:18546581..18551368-chr11:18654825..18657467,6	K562	blood:
3	chr11:18502477..18505271-chr11:18547847..18549412,2	K562	blood:
4	chr11:18341846..18344494-chr11:18547115..18549354,2	MCF-7	breast:
5	chr11:18432193..18433875-chr11:18547475..18550164,2	MCF-7	breast:
6	chr11:18547238..18549661-chr11:18600782..18603302,3	MCF-7	breast:
7	chr11:18548103..18548963-chr18:12702273..12702811,2	Hela-S3	cervix:
8	chr11:18414795..18417618-chr11:18546727..18549809,4	MCF-7	breast:
9	chr11:18546303..18549278-chr11:18609985..18612598,2	K562	blood:
10	chr11:18548392..18548985-chr16:58231117..58232045,2	Hela-S3	cervix:
11	chr11:18548256..18548930-chr9:130953663..130954444,2	Hela-S3	cervix:
12	chr11:18343253..18347316-chr11:18546908..18550670,5	K562	blood:
13	chr1:36396047..36396934-chr11:18547924..18549049,4	Hela-S3	cervix:
14	chr11:18531181..18534158-chr11:18547173..18549352,2	MCF-7	breast:
15	chr10:70091815..70092544-chr11:18548061..18548917,2	Hela-S3	cervix:
16	chr11:18415765..18417941-chr11:18547561..18549649,2	K562	blood:
17	chr11:18546489..18551340-chr11:18552893..18563258,14	MCF-7	breast:
18	chr11:18414231..18417142-chr11:18548434..18550099,2	K562	blood:
19	chr11:18548173..18549021-chr5:1633797..1634587,2	Hela-S3	cervix:
20	chr11:18548430..18549296-chr17:72199825..72200786,2	Hela-S3	cervix:
21	chr11:18415399..18418482-chr11:18547632..18550708,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LDHAL6A-1	chr11:18548579-18550760	NONHSAT018294

Variant related genes	Relation type
TSG101	TF binding region
ENSG00000126070	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000188002	Chromatin interaction
ENSG00000074319	Chromatin interaction
ENSG00000110768	Chromatin interaction
ENSG00000166796	Chromatin interaction
ENSG00000096746	Chromatin interaction
ENSG00000172809	Chromatin interaction
ENSG00000151116	Chromatin interaction
ENSG00000070770	Chromatin interaction
ENSG00000179119	Chromatin interaction
ENSG00000134333	Chromatin interaction
ENSG00000148337	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000110756	Chromatin interaction
ENSG00000256361	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10219146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12283473	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16935424	1.00[JPT][hapmap]
rs16935432	1.00[JPT][hapmap]
rs16935557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17392588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1973412	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056781	1.00[JPT][hapmap]
rs2271079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2643868	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2658547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2896526	1.00[JPT][hapmap]
rs35593189	1.00[JPT][hapmap]
rs3740713	1.00[JPT][hapmap]
rs72871724	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72871727	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72871772	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72876735	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72876768	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72876784	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv1038015	chr11:18435855-18558211	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	nsv1046886	chr11:18547568-18781448	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv540956	chr11:18547568-18781448	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18547000-18549000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr11:18547000-18549200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:18547000-18549600	Active TSS	GM12878-XiMat	blood
4	chr11:18547200-18549000	Active TSS	Muscle Satellite Cultured Cells	--
5	chr11:18547200-18549000	Active TSS	Brain Substantia Nigra	brain
6	chr11:18547200-18549000	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr11:18547200-18549000	Active TSS	Fetal Stomach	stomach
8	chr11:18547200-18549200	Active TSS	Fetal Brain Female	brain
9	chr11:18547200-18549400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:18547200-18549600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr11:18547200-18549600	Active TSS	H1 Cell Line	embryonic stem cell
12	chr11:18547200-18549600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:18547200-18549600	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr11:18547200-18549600	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr11:18547200-18549600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:18547200-18549600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:18547200-18549600	Active TSS	Fetal Intestine Large	intestine
18	chr11:18547200-18549600	Active TSS	K562	blood
19	chr11:18547200-18549800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:18547200-18549800	Active TSS	Psoas Muscle	Psoas
21	chr11:18547200-18549800	Active TSS	Stomach Smooth Muscle	stomach
22	chr11:18547400-18549000	Active TSS	Fetal Muscle Leg	muscle
23	chr11:18547400-18549000	Active TSS	Fetal Thymus	thymus
24	chr11:18547400-18549200	Active TSS	Placenta	Placenta
25	chr11:18547400-18549400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr11:18547400-18549400	Active TSS	H9 Cell Line	embryonic stem cell
27	chr11:18547400-18549400	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr11:18547400-18549400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:18547400-18549400	Active TSS	Colonic Mucosa	Colon
30	chr11:18547400-18549400	Active TSS	Fetal Intestine Small	intestine
31	chr11:18547400-18549400	Active TSS	Fetal Muscle Trunk	muscle
32	chr11:18547400-18549400	Active TSS	Ovary	ovary
33	chr11:18547400-18549400	Active TSS	Right Atrium	heart
34	chr11:18547400-18549600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr11:18547400-18549600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr11:18547400-18549600	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr11:18547400-18549600	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr11:18547400-18549600	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr11:18547400-18549600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:18547400-18549600	Active TSS	HSMMtube	muscle
41	chr11:18547400-18549800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr11:18547400-18549800	Active TSS	Right Ventricle	heart
43	chr11:18547400-18549800	Active TSS	A549	lung
44	chr11:18547600-18549000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr11:18547600-18549000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr11:18547600-18549000	Active TSS	Brain Anterior Caudate	brain
47	chr11:18547600-18549000	Active TSS	Colon Smooth Muscle	Colon
48	chr11:18547600-18549000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr11:18547600-18549000	Active TSS	Fetal Heart	heart
50	chr11:18547600-18549000	Active TSS	Rectal Mucosa Donor 29	rectum

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