Variant report

Variant	rs719668
Chromosome Location	chr2:113342566-113342567
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	BHLHE40	chr2:113341121-113342596	K562	blood:	n/a	n/a
2	CHD2	chr2:113341713-113342622	K562	blood:	n/a	chr2:113342420-113342430
3	CREB1	chr2:113340867-113342678	HepG2	liver:	n/a	n/a
4	TAF1	chr2:113341389-113342697	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr2:113341035-113342697	HepG2	liver:	n/a	n/a
6	ELF1	chr2:113341421-113342642	HepG2	liver:	n/a	chr2:113341940-113341953 chr2:113341971-113341984
7	REST	chr2:113341163-113342631	HL-60	blood:	n/a	n/a
8	TAF1	chr2:113342211-113342598	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr2:113341634-113342706	GM15510	blood:	n/a	n/a
10	POLR2A	chr2:113341428-113342877	Hela-S3	cervix:	n/a	n/a
11	MTA3	chr2:113341029-113342926	GM12878	blood:	n/a	n/a
12	MXI1	chr2:113341045-113342848	HepG2	liver:	n/a	chr2:113342149-113342164
13	TBP	chr2:113341725-113342636	Hela-S3	cervix:	n/a	n/a
14	YY1	chr2:113341310-113342615	GM12878	blood:	n/a	chr2:113342147-113342156 chr2:113342067-113342076
15	POLR2A	chr2:113339455-113342662	K562	blood:	n/a	n/a
16	ELF1	chr2:113341391-113342619	MCF-7	breast:	n/a	chr2:113341940-113341953 chr2:113341971-113341984
17	JUND	chr2:113341615-113342586	A549	lung:	n/a	n/a
18	TCF7L2	chr2:113341570-113342586	HCT-116	colon:	n/a	n/a
19	POU2F2	chr2:113341541-113342610	GM12878	blood:	n/a	n/a
20	SIN3AK20	chr2:113341645-113342597	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr2:113341022-113342876	U87	brain:	n/a	n/a
22	TAF1	chr2:113341635-113342648	PFSK-1	brain:	n/a	n/a
23	STAT5A	chr2:113341421-113342584	GM12878	blood:	n/a	n/a
24	SIX5	chr2:113341590-113342762	A549	lung:	n/a	n/a
25	MAX	chr2:113341452-113342712	A549	lung:	n/a	chr2:113342155-113342164 chr2:113342399-113342409
26	JUND	chr2:113341797-113342566	HepG2	liver:	n/a	n/a
27	POLR2A	chr2:113340936-113342770	MCF-7	breast:	n/a	n/a
28	POLR2A	chr2:113341403-113342724	U87	brain:	n/a	n/a
29	POLR2A	chr2:113341635-113342628	SK-N-MC	brain:	n/a	n/a
30	MYC	chr2:113341505-113342583	NB4	blood:	n/a	chr2:113342155-113342164 chr2:113342399-113342409
31	POLR2A	chr2:113341555-113342567	HepG2	liver:	n/a	n/a
32	TEAD4	chr2:113341609-113342707	K562	blood:	n/a	n/a
33	BHLHE40	chr2:113341669-113342567	HepG2	liver:	n/a	n/a
34	POLR2A	chr2:113341582-113343043	PFSK-1	brain:	n/a	n/a
35	MAZ	chr2:113341728-113342644	GM12878	blood:	n/a	chr2:113342155-113342164 chr2:113342399-113342409
36	MAX	chr2:113341733-113342601	K562	blood:	n/a	chr2:113342155-113342164 chr2:113342399-113342409
37	POLR2A	chr2:113341551-113342585	H1-neurons	neurons:	n/a	n/a
38	CREB1	chr2:113341717-113342572	A549	lung:	n/a	n/a
39	MYBL2	chr2:113340800-113343015	HepG2	liver:	n/a	n/a
40	FOSL2	chr2:113341624-113342821	HepG2	liver:	n/a	n/a
41	POLR2A	chr2:113341219-113342864	K562	blood:	n/a	n/a
42	MAZ	chr2:113341691-113342618	K562	blood:	n/a	chr2:113342155-113342164 chr2:113342399-113342409
43	CUX1	chr2:113341736-113342612	K562	blood:	n/a	n/a
44	TAF1	chr2:113341494-113342709	MCF-7	breast:	n/a	n/a
45	POLR2A	chr2:113342079-113342623	H1-hESC	embryonic stem cell:	n/a	n/a
46	MAX	chr2:113341581-113342668	SK-N-SH	brain:	n/a	chr2:113342155-113342164 chr2:113342399-113342409
47	POLR2A	chr2:113341474-113342695	HepG2	liver:	n/a	n/a
48	SP1	chr2:113341802-113342605	H1-hESC	embryonic stem cell:	n/a	chr2:113342399-113342413 chr2:113342399-113342409 chr2:113342399-113342408 chr2:113342400-113342409 chr2:113342398-113342410 chr2:113342398-113342410
49	POLR2A	chr2:113340882-113342926	GM12878	blood:	n/a	n/a
50	POLR2A	chr2:113341384-113342664	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:99078212..99079127-chr2:113342181..113342990,2	Hela-S3	cervix:
2	chr2:113342174..113343883-chr2:113403461..113405044,2	K562	blood:
3	chr10:75006774..75007379-chr2:113341862..113342735,2	Hela-S3	cervix:
4	chr2:39351098..39351964-chr2:113341975..113342944,2	NB4	blood:
5	chr12:46760893..46761645-chr2:113341924..113342581,2	Hela-S3	cervix:
6	chr2:113335699..113339674-chr2:113340106..113343204,5	K562	blood:
7	chr2:113298954..113302477-chr2:113339455..113343767,5	MCF-7	breast:
8	chr2:113342510..113344437-chr2:113651250..113653348,2	MCF-7	breast:
9	chr2:113296892..113302637-chr2:113340004..113344909,8	K562	blood:
10	chr2:113340008..113343992-chr2:113483304..113487579,6	K562	blood:
11	chr2:113031869..113034952-chr2:113341167..113343629,3	MCF-7	breast:
12	chr2:113340774..113345524-chr2:113480391..113485957,9	MCF-7	breast:
13	chr1:212208449..212209308-chr2:113342043..113342672,2	Hela-S3	cervix:
14	chr2:113339547..113343883-chr2:113402286..113405078,6	K562	blood:
15	chr2:113237331..113240789-chr2:113339342..113343125,4	K562	blood:
16	chr2:113340479..113344233-chr2:113401874..113407323,6	MCF-7	breast:
17	chr2:113338959..113342918-chr2:113483353..113487579,5	K562	blood:
18	chr2:113298569..113302646-chr2:113339335..113343133,7	K562	blood:
19	chr17:2303358..2303980-chr2:113342107..113342737,2	Hela-S3	cervix:
20	chr2:113340437..113343949-chr2:113401268..113406617,9	MCF-7	breast:
21	chr2:113298759..113301838-chr2:113339526..113343252,4	MCF-7	breast:
22	chr2:113235824..113243298-chr2:113338675..113344022,16	MCF-7	breast:
23	chr2:113307316..113310204-chr2:113340273..113342615,2	MCF-7	breast:
24	chr2:113010958..113014005-chr2:113340303..113342675,3	K562	blood:

Variant related genes	Relation type
ENSG00000243389	TF binding region
ENSG00000125630	Chromatin interaction
ENSG00000144130	Chromatin interaction
ENSG00000237753	Chromatin interaction
ENSG00000143476	Chromatin interaction
ENSG00000115904	Chromatin interaction
ENSG00000236756	Chromatin interaction
ENSG00000114999	Chromatin interaction
ENSG00000207383	Chromatin interaction
ENSG00000188177	Chromatin interaction
ENSG00000144136	Chromatin interaction
ENSG00000143493	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000144161	Chromatin interaction
ENSG00000070444	Chromatin interaction
ENSG00000165879	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10153558	0.85[CEU][hapmap]
rs11123140	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11123141	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11675730	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11687159	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1437673	0.82[YRI][hapmap]
rs2304555	0.95[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs3748024	0.81[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs3789722	0.96[ASN][1000 genomes]
rs3816140	0.88[ASW][hapmap];0.95[CEU][hapmap];0.84[GIH][hapmap];0.93[LWK][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs3961775	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs719667	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7607358	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]

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	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers 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	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs719668	FBLN7	cis	parietal	SCAN
rs719668	POLR1B	cis	cerebellum	SCAN
rs719668	POLR1B	cis	Skin Sun Exposed Lower leg	GTEx
rs719668	POLR1B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113340800-113342600	Active TSS	Fetal Brain Male	brain
2	chr2:113340800-113342800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:113340800-113342800	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr2:113340800-113343000	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr2:113341000-113342600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:113341000-113342600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr2:113341000-113342600	Active TSS	Psoas Muscle	Psoas
8	chr2:113341000-113342800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr2:113341000-113342800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:113341000-113343000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr2:113341000-113343400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:113341200-113342600	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr2:113341200-113342600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:113341200-113342600	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr2:113341200-113342600	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr2:113341200-113342600	Active TSS	Left Ventricle	heart
17	chr2:113341200-113342600	Active TSS	Lung	lung
18	chr2:113341200-113342600	Active TSS	Right Ventricle	heart
19	chr2:113341200-113342800	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr2:113341200-113342800	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr2:113341200-113342800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:113341200-113343000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:113341200-113343000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr2:113341200-113343200	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr2:113341200-113343400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr2:113341400-113342600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:113341400-113342600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:113341400-113342600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:113341400-113342600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:113341400-113342600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:113341400-113342600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:113341400-113342600	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr2:113341400-113342600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:113341400-113342600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:113341400-113342600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:113341400-113342600	Active TSS	Brain Anterior Caudate	brain
37	chr2:113341400-113342600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:113341400-113342600	Active TSS	Fetal Intestine Large	intestine
39	chr2:113341400-113342600	Active TSS	Fetal Intestine Small	intestine
40	chr2:113341400-113342600	Active TSS	Fetal Kidney	kidney
41	chr2:113341400-113342600	Active TSS	Gastric	stomach
42	chr2:113341400-113342600	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr2:113341400-113342600	Active TSS	Spleen	Spleen
44	chr2:113341400-113342600	Bivalent/Poised TSS	HepG2	liver
45	chr2:113341400-113342600	Active TSS	HSMM	muscle
46	chr2:113341400-113342600	Active TSS	NHDF-Ad	bronchial
47	chr2:113341400-113342800	Active TSS	H1 Cell Line	embryonic stem cell
48	chr2:113341400-113342800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:113341400-113342800	Active TSS	Aorta	Aorta
50	chr2:113341400-113342800	Active TSS	Pancreatic Islets	Pancreatic Islet

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