Variant report

Variant	rs35669602
Chromosome Location	chr19:41100624-41100625
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	chr19:41100600-41100750	K562	blood:	n/a	n/a
2	MAX	chr19:41100165-41101354	A549	lung:	n/a	chr19:41100945-41100955
3	CTCF	chr19:41100622-41100799	K562	blood:	n/a	n/a
4	CTCF	chr19:41100580-41100730	Hela-S3	cervix:	n/a	n/a
5	GABPA	chr19:41100058-41100802	A549	lung:	n/a	n/a
6	CTCF	chr19:41100620-41100770	SK-N-SH_RA	brain:	n/a	n/a
7	ZBTB7A	chr19:41100533-41100984	K562	blood:	n/a	n/a
8	CTCF	chr19:41100620-41100770	AG09309	skin:	n/a	n/a
9	CTCF	chr19:41100598-41100826	Gliobla	brain:	n/a	n/a
10	MAX	chr19:41100548-41101118	K562	blood:	n/a	chr19:41100945-41100955
11	CTCF	chr19:41100600-41100750	BE2_C	brain:	n/a	n/a
12	POLR2A	chr19:41100135-41100988	U87	brain:	n/a	n/a
13	CTCF	chr19:41100620-41100770	HA-sp	spinal cord:	n/a	n/a
14	POLR2A	chr19:41100570-41100750	MCF-7	breast:	n/a	n/a
15	CTCF	chr19:41100617-41100821	MCF-7	breast:	n/a	n/a
16	CTCF	chr19:41100620-41100770	HPAF	blood vessel:	n/a	n/a
17	FOS	chr19:41100614-41100914	MCF10A-Er-Src	breast:	n/a	chr19:41100742-41100750 chr19:41100740-41100752 chr19:41100738-41100749 chr19:41100741-41100751
18	CTCF	chr19:41100621-41100811	NHEK	skin:	n/a	n/a
19	CTCF	chr19:41100600-41100750	HCM	heart:	n/a	n/a
20	FOSL1	chr19:41100531-41100831	K562	blood:	n/a	chr19:41100742-41100750 chr19:41100740-41100752 chr19:41100738-41100749 chr19:41100741-41100751
21	CTCF	chr19:41100620-41100770	AG09319	gingival:	n/a	n/a
22	CTCF	chr19:41100520-41100670	HRPEpiC	eye:	n/a	n/a
23	CTCF	chr19:41100600-41100750	AG04449	skin:	n/a	n/a
24	CTCF	chr19:41100596-41100919	K562	blood:	n/a	n/a
25	FOS	chr19:41100572-41100881	MCF10A-Er-Src	breast:	n/a	chr19:41100742-41100750 chr19:41100740-41100752 chr19:41100738-41100749 chr19:41100741-41100751
26	GABPA	chr19:41100114-41100629	A549	lung:	n/a	n/a
27	BCL3	chr19:41100048-41101329	A549	lung:	n/a	chr19:41100339-41100348 chr19:41100781-41100790
28	FOSL2	chr19:41100553-41100926	A549	lung:	n/a	chr19:41100742-41100750 chr19:41100740-41100752 chr19:41100738-41100749 chr19:41100741-41100751
29	CTCF	chr19:41100620-41100770	HCFaa	heart:	n/a	n/a
30	YY1	chr19:41100601-41100792	K562	blood:	n/a	n/a
31	ELF1	chr19:41100112-41100751	K562	blood:	n/a	n/a
32	POLR2A	chr19:41100068-41100652	H1-neurons	neurons:	n/a	n/a
33	CTCF	chr19:41100600-41100750	HEEpiC	esophagus:	n/a	n/a
34	CTCF	chr19:41100600-41100750	HA-sp	spinal cord:	n/a	n/a
35	POLR2A	chr19:41100601-41100704	K562	blood:	n/a	n/a
36	CTCF	chr19:41100614-41100854	K562	blood:	n/a	n/a
37	MYC	chr19:41100575-41101109	K562	blood:	n/a	chr19:41100945-41100955
38	CTCF	chr19:41100600-41100750	A549	lung:	n/a	n/a
39	FOS	chr19:41100586-41100909	MCF10A-Er-Src	breast:	n/a	chr19:41100742-41100750 chr19:41100740-41100752 chr19:41100738-41100749 chr19:41100741-41100751
40	CTCF	chr19:41100600-41100750	HPF	lung:	n/a	n/a
41	CTCF	chr19:41100597-41100884	K562	blood:	n/a	n/a
42	JUND	chr19:41100619-41100904	K562	blood:	n/a	chr19:41100742-41100750 chr19:41100740-41100752 chr19:41100738-41100749 chr19:41100741-41100751
43	CTCF	chr19:41100520-41100670	NHLF	lung:	n/a	n/a
44	CTCF	chr19:41100600-41100750	NHDF-neo	bronchial:	n/a	n/a
45	CREB1	chr19:41100519-41101149	A549	lung:	n/a	n/a
46	MAX	chr19:41100266-41101228	A549	lung:	n/a	chr19:41100945-41100955
47	RAD21	chr19:41100576-41100869	Hela-S3	cervix:	n/a	n/a
48	REST	chr19:41100209-41100942	A549	lung:	n/a	chr19:41100837-41100850 chr19:41100428-41100441 chr19:41100830-41100843
49	CTCF	chr19:41100576-41100824	IMR90	lung:	n/a	n/a
50	CEBPB	chr19:41100273-41100874	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40948223..40951399-chr19:41100513..41104736,3	MCF-7	breast:
2	chr19:41093850..41097927-chr19:41099715..41103880,5	K562	blood:
3	chr19:41087979..41091275-chr19:41098562..41102111,3	MCF-7	breast:

Variant related genes	Relation type
LTBP4	TF binding region
ENSG00000160410	Chromatin interaction
ENSG00000268366	Chromatin interaction
ENSG00000167565	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12977500	1.00[ASN][1000 genomes]
rs1864077	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56013937	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911714	chr19:41006426-41165252	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv911715	chr19:41014922-41141434	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv911716	chr19:41023511-41109456	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv911717	chr19:41023511-41141434	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv911719	chr19:41033109-41147087	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv911720	chr19:41033109-41156940	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv911721	chr19:41040334-41124931	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	nsv869561	chr19:41077513-41139834	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
13	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
14	nsv911724	chr19:41089505-41165252	Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
15	nsv911725	chr19:41090190-41114065	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
16	nsv911726	chr19:41090190-41141434	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
17	esv3353715	chr19:41100494-41100719	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35669602	LTBP4	cis	multi-tissue	Pritchard

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41083600-41101000	Weak transcription	HSMMtube	muscle
2	chr19:41084600-41102600	Weak transcription	Right Atrium	heart
3	chr19:41087600-41102600	Weak transcription	Small Intestine	intestine
4	chr19:41094400-41102400	Weak transcription	Fetal Lung	lung
5	chr19:41094600-41101200	Weak transcription	Primary B cells from cord blood	blood
6	chr19:41094600-41102800	Weak transcription	Aorta	Aorta
7	chr19:41094600-41102800	Weak transcription	Left Ventricle	heart
8	chr19:41095200-41101000	Weak transcription	NHEK	skin
9	chr19:41095200-41102400	Weak transcription	HUVEC	blood vessel
10	chr19:41095200-41103200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr19:41097000-41102600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:41097000-41102600	Weak transcription	Right Ventricle	heart
13	chr19:41097400-41102600	Weak transcription	Lung	lung
14	chr19:41097400-41102800	Weak transcription	Ovary	ovary
15	chr19:41097400-41102800	Weak transcription	Spleen	Spleen
16	chr19:41097600-41100800	Weak transcription	Thymus	Thymus
17	chr19:41099800-41101000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr19:41099800-41101200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr19:41100000-41101000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:41100000-41101000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr19:41100000-41101000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:41100000-41101000	Active TSS	Fetal Brain Female	brain
23	chr19:41100000-41101200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr19:41100200-41100800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:41100200-41100800	Weak transcription	Fetal Heart	heart
26	chr19:41100200-41101000	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr19:41100200-41101000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr19:41100200-41101000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr19:41100200-41101000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr19:41100200-41101000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:41100200-41101200	Enhancers	H1 Cell Line	embryonic stem cell
32	chr19:41100200-41101200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:41100200-41101200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:41100200-41101200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
35	chr19:41100200-41101200	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr19:41100200-41101200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr19:41100200-41101200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr19:41100200-41101200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr19:41100200-41101200	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr19:41100200-41101600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr19:41100200-41102000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr19:41100400-41100800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
43	chr19:41100400-41100800	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr19:41100400-41100800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
45	chr19:41100400-41100800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:41100400-41100800	Active TSS	Brain Cingulate Gyrus	brain
47	chr19:41100400-41100800	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr19:41100400-41100800	Flanking Active TSS	Fetal Brain Male	brain
49	chr19:41100400-41100800	Bivalent Enhancer	Fetal Stomach	stomach
50	chr19:41100400-41100800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle

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