Variant report

Variant	rs9989160
Chromosome Location	chr14:34932148-34932149
allele	A/C
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	chr14:34930136-34932486	GM12891	blood:	n/a	n/a
2	POLR2A	chr14:34930594-34932204	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr14:34930572-34932439	K562	blood:	n/a	n/a
4	REST	chr14:34930943-34932376	H1-neurons	neurons:	n/a	n/a
5	RCOR1	chr14:34930787-34932246	K562	blood:	n/a	n/a
6	EP300	chr14:34930823-34932312	HepG2	liver:	n/a	chr14:34931196-34931205 chr14:34931179-34931195 chr14:34932166-34932179
7	MYC	chr14:34930572-34932347	NB4	blood:	n/a	n/a
8	TBL1XR1	chr14:34931739-34932175	GM12878	blood:	n/a	n/a
9	SMC3	chr14:34931797-34932375	Hela-S3	cervix:	n/a	n/a
10	ELK1	chr14:34931991-34932179	GM12878	blood:	n/a	n/a
11	SMC3	chr14:34931874-34932412	HepG2	liver:	n/a	n/a
12	MAX	chr14:34931081-34932513	A549	lung:	n/a	n/a
13	MAX	chr14:34930777-34932172	K562	blood:	n/a	n/a
14	RUNX3	chr14:34931763-34932294	GM12878	blood:	n/a	n/a
15	RFX5	chr14:34931267-34932280	HepG2	liver:	n/a	n/a
16	POLR2A	chr14:34931138-34932160	A549	lung:	n/a	n/a
17	POLR2A	chr14:34930575-34932508	Raji	blood:	n/a	n/a
18	MAX	chr14:34930298-34932329	NB4	blood:	n/a	n/a
19	MAZ	chr14:34930826-34932314	HepG2	liver:	n/a	n/a
20	POLR2A	chr14:34930946-34932316	GM12878	blood:	n/a	n/a
21	KAP1	chr14:34931798-34932363	U2OS	brain:	n/a	n/a
22	MYC	chr14:34930407-34932209	K562	blood:	n/a	n/a
23	TCF12	chr14:34931603-34932484	A549	lung:	n/a	chr14:34931928-34931935
24	POLR2A	chr14:34930815-34932380	GM12892	blood:	n/a	n/a
25	EGR1	chr14:34931262-34932279	HCT-116	colon:	n/a	chr14:34931666-34931676 chr14:34931664-34931678 chr14:34931666-34931675 chr14:34931666-34931676
26	SIN3A	chr14:34930476-34932355	H1-hESC	embryonic stem cell:	n/a	chr14:34931692-34931705
27	RCOR1	chr14:34931815-34932212	K562	blood:	n/a	n/a
28	CEBPD	chr14:34930771-34932368	HepG2	liver:	n/a	n/a
29	POLR2A	chr14:34931152-34932171	PBDE	blood:	n/a	n/a
30	NR2F2	chr14:34930422-34932189	MCF-7	breast:	n/a	chr14:34930887-34930902
31	TBL1XR1	chr14:34931956-34932221	K562	blood:	n/a	n/a
32	MXI1	chr14:34929832-34932603	IMR90	lung:	n/a	n/a
33	HDAC2	chr14:34930570-34932355	HepG2	liver:	n/a	n/a
34	CHD2	chr14:34930644-34932302	Hela-S3	cervix:	n/a	n/a
35	TCF7L2	chr14:34931996-34932405	Hela-S3	cervix:	n/a	n/a
36	CHD2	chr14:34931293-34932195	H1-hESC	embryonic stem cell:	n/a	n/a
37	MYBL2	chr14:34930390-34932519	HepG2	liver:	n/a	n/a
38	MAZ	chr14:34930829-34932529	IMR90	lung:	n/a	n/a
39	HA-E2F1	chr14:34930751-34932187	MCF-7	breast:	n/a	chr14:34931416-34931427 chr14:34930942-34930951 chr14:34931226-34931236
40	MTA3	chr14:34931713-34932345	GM12878	blood:	n/a	n/a
41	TAF1	chr14:34930843-34932202	HepG2	liver:	n/a	n/a
42	POLR2A	chr14:34930207-34932387	GM18505	blood:	n/a	n/a
43	MAX	chr14:34931138-34932210	SK-N-SH	brain:	n/a	n/a
44	RCOR1	chr14:34930772-34932347	HepG2	liver:	n/a	n/a
45	POLR2A	chr14:34931776-34932187	H1-hESC	embryonic stem cell:	n/a	n/a
46	CREB1	chr14:34930559-34932363	HepG2	liver:	n/a	n/a
47	POLR2A	chr14:34930625-34932410	HepG2	liver:	n/a	n/a
48	POLR2A	chr14:34931153-34932315	SK-N-SH	brain:	n/a	n/a
49	TBL1XR1	chr14:34931912-34932228	K562	blood:	n/a	n/a
50	BACH1	chr14:34930764-34932380	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:34930470..34932730-chr14:35007965..35010227,2	K562	blood:
2	chr14:34929915..34933661-chr14:35006959..35010400,6	MCF-7	breast:
3	chr14:34930543..34933153-chr14:35015586..35017251,2	MCF-7	breast:
4	chr14:34929666..34933656-chr14:35005721..35010391,9	K562	blood:
5	chr14:34931690..34933656-chr14:35005412..35007221,2	K562	blood:
6	chr14:34931264..34933781-chr14:35036806..35039605,2	K562	blood:

Variant related genes	Relation type
SPTSSA	TF binding region
EGLN3	TF binding region
ENSG00000240463	Chromatin interaction
ENSG00000129518	Chromatin interaction
ENSG00000206596	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10132233	0.89[CEU][hapmap];0.88[JPT][hapmap]
rs10137714	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs12432137	0.89[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2002517	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs2383633	0.89[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap]
rs2383634	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs4982180	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4982183	0.89[CEU][hapmap]
rs7154588	0.89[CEU][hapmap];0.82[JPT][hapmap]
rs9806112	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040980	chr14:34345018-35255592	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv1051104	chr14:34592378-35007083	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv949738	chr14:34616331-34990688	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv564192	chr14:34725233-34996507	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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	13 gene(s)	inside rSNPs	diseases
5	nsv564193	chr14:34728127-35000188	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers 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 target site	13 gene(s)	inside rSNPs	diseases
6	nsv528989	chr14:34744426-34998705	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1054949	chr14:34834260-34992049	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv542025	chr14:34834260-34992049	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv1050218	chr14:34851521-34969433	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv1048369	chr14:34886956-34974774	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv901600	chr14:34895977-35010041	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	esv3401129	chr14:34930451-34932699	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv78136	chr14:34932149-34932150	Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9989160	FHL2	trans	lymphoblastoid	seeQTL
rs9989160	SRP54	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:34929000-34932400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr14:34929000-34932600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr14:34929200-34932400	Active TSS	HMEC	breast
4	chr14:34929400-34932400	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr14:34929800-34932200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr14:34929800-34932200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr14:34929800-34932200	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr14:34929800-34932200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr14:34929800-34932200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr14:34929800-34932200	Active TSS	Psoas Muscle	Psoas
11	chr14:34929800-34932200	Active TSS	A549	lung
12	chr14:34929800-34932200	Active TSS	HSMMtube	muscle
13	chr14:34930000-34932200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr14:34930000-34932200	Active TSS	Aorta	Aorta
15	chr14:34930200-34932200	Active TSS	H9 Cell Line	embryonic stem cell
16	chr14:34930400-34932200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr14:34930400-34932200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr14:34930400-34932200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr14:34930400-34932200	Active TSS	Fetal Thymus	thymus
20	chr14:34930400-34932200	Active TSS	GM12878-XiMat	blood
21	chr14:34930600-34932200	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr14:34930600-34932400	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr14:34930800-34932200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr14:34930800-34932200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr14:34930800-34932200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr14:34930800-34932200	Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr14:34930800-34932200	Active TSS	Brain Cingulate Gyrus	brain
28	chr14:34930800-34932200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr14:34930800-34932200	Active TSS	Colon Smooth Muscle	Colon
30	chr14:34930800-34932200	Active TSS	Gastric	stomach
31	chr14:34930800-34932200	Active TSS	Rectal Mucosa Donor 31	rectum
32	chr14:34930800-34932400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr14:34930800-34932400	Active TSS	Brain Substantia Nigra	brain
34	chr14:34930800-34932400	Active TSS	Fetal Kidney	kidney
35	chr14:34930800-34932600	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr14:34931000-34932200	Active TSS	Primary T cells from cord blood	blood
37	chr14:34931000-34932400	Active TSS	Brain Anterior Caudate	brain
38	chr14:34931000-34932400	Active TSS	Fetal Brain Female	brain
39	chr14:34931800-34932200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr14:34931800-34932200	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr14:34931800-34932200	Flanking Active TSS	Primary B cells from peripheral blood	blood
42	chr14:34931800-34932200	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr14:34931800-34932200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr14:34931800-34932200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr14:34931800-34932200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr14:34931800-34932200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr14:34931800-34932200	Flanking Active TSS	Liver	Liver
48	chr14:34931800-34932200	Flanking Active TSS	Colonic Mucosa	Colon
49	chr14:34931800-34932200	Flanking Active TSS	Esophagus	oesophagus
50	chr14:34931800-34932200	Flanking Active TSS	Fetal Heart	heart

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