Variant report

Variant	rs7256866
Chromosome Location	chr19:35771257-35771258
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	POLR2A	chr19:35770772-35771289	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:35771122-35771350	MCF-7	breast:	n/a	n/a
3	POLR2A	chr19:35770681-35772468	GM12892	blood:	n/a	n/a
4	PML	chr19:35771230-35772376	GM12878	blood:	n/a	n/a
5	EP300	chr19:35770799-35771312	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:35770727-35771416	A549	lung:	n/a	n/a
7	POLR2A	chr19:35769553-35772534	K562	blood:	n/a	n/a
8	POLR2A	chr19:35770718-35771368	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:35770671-35771735	HepG2	liver:	n/a	n/a
10	POLR2A	chr19:35770890-35771297	A549	lung:	n/a	n/a
11	STAT5A	chr19:35771001-35772465	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:35770753-35772570	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr19:35770903-35772628	GM12891	blood:	n/a	n/a
14	YY1	chr19:35770844-35771348	HepG2	liver:	n/a	chr19:35771169-35771180
15	POLR2A	chr19:35770845-35771363	HepG2	liver:	n/a	n/a
16	POLR2A	chr19:35770903-35772185	GM12891	blood:	n/a	n/a
17	POLR2A	chr19:35771054-35771368	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr19:35770904-35772275	PANC-1	pancreas:	n/a	n/a
19	POLR2A	chr19:35770689-35771382	GM12878	blood:	n/a	n/a
20	CHD2	chr19:35771211-35771447	Hela-S3	cervix:	n/a	n/a
21	NFIC	chr19:35770817-35771289	HepG2	liver:	n/a	n/a
22	POLR2A	chr19:35770315-35772079	HepG2	liver:	n/a	n/a
23	ELF1	chr19:35771203-35771694	GM12878	blood:	n/a	n/a
24	POLR2A	chr19:35771193-35771880	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr19:35770750-35771267	K562	blood:	n/a	n/a
26	CEBPB	chr19:35771004-35771368	HepG2	liver:	n/a	n/a
27	POLR2A	chr19:35770381-35772592	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:35771055-35771896	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr19:35770869-35771317	U87	brain:	n/a	n/a
30	EP300	chr19:35770654-35771393	HepG2	liver:	n/a	chr19:35771377-35771390
31	POLR2A	chr19:35770782-35772559	GM12878	blood:	n/a	n/a
32	MAX	chr19:35770546-35771882	HepG2	liver:	n/a	chr19:35771624-35771635 chr19:35771623-35771638 chr19:35771185-35771194 chr19:35771624-35771635 chr19:35771625-35771634 chr19:35771624-35771635
33	PBX3	chr19:35770729-35772616	A549	lung:	n/a	n/a
34	BCL3	chr19:35770882-35772280	A549	lung:	n/a	n/a
35	MYBL2	chr19:35770772-35771340	HepG2	liver:	n/a	n/a
36	SP1	chr19:35770709-35771317	HepG2	liver:	n/a	n/a
37	MAZ	chr19:35770870-35771264	HepG2	liver:	n/a	chr19:35771185-35771194
38	POLR2A	chr19:35770734-35772371	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr19:35770684-35771418	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:35770723-35772481	HepG2	liver:	n/a	n/a
41	POLR2A	chr19:35771002-35771321	HepG2	liver:	n/a	n/a
42	RAD21	chr19:35770931-35771297	HepG2	liver:	n/a	n/a
43	HNF4G	chr19:35770785-35771366	HepG2	liver:	n/a	chr19:35771168-35771180 chr19:35771168-35771181 chr19:35771163-35771185 chr19:35771167-35771181 chr19:35771063-35771085 chr19:35771167-35771180 chr19:35771168-35771181 chr19:35771168-35771180 chr19:35770934-35770941
44	POLR2A	chr19:35770867-35772321	GM12878	blood:	n/a	n/a
45	POLR2A	chr19:35770723-35771417	ECC-1	luminal epithelium:	n/a	n/a
46	HNF4A	chr19:35770756-35771324	HepG2	liver:	n/a	chr19:35771168-35771180 chr19:35771166-35771181 chr19:35771168-35771181 chr19:35771163-35771185 chr19:35771167-35771181 chr19:35771063-35771085 chr19:35771167-35771180 chr19:35771168-35771181 chr19:35771168-35771180 chr19:35770934-35770941
47	POLR2A	chr19:35771057-35771336	HCT-116	colon:	n/a	n/a
48	POLR2A	chr19:35771150-35771693	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr19:35770775-35772509	MCF-7	breast:	n/a	n/a
50	EP300	chr19:35770820-35771344	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:35758290..35762202-chr19:35770035..35773582,5	K562	blood:
2	chr19:35769830..35774693-chr19:35781606..35784141,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USF2-1	chr19:35771149-35771258	NONHSAT065817

Variant related genes	Relation type
HAMP	TF binding region
ENSG00000105695	Chromatin interaction
ENSG00000105698	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10405246	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410675	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10414846	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10419261	0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10419959	0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10421096	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421504	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421768	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424619	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1052033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12973672	0.93[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12974791	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979058	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12979792	0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12981527	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12984022	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12985618	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12986033	1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13345192	0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073899	0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280744	1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280745	1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28365133	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28365136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34832786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35250673	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35497966	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35959789	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564117	0.81[TSI][hapmap]
rs62109572	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112772	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71352913	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8101606	0.93[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv911618	chr19:35734107-35807845	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
8	esv1836312	chr19:35741456-35786868	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	n/a
9	nsv911619	chr19:35749563-35775441	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
10	nsv911620	chr19:35752917-35771382	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
11	nsv911621	chr19:35752917-35772471	Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers 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 miRNA target site	30 gene(s)	inside rSNPs	n/a
12	nsv911622	chr19:35752917-35773146	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
13	nsv911623	chr19:35752917-35775441	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
14	nsv911624	chr19:35759043-35771382	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7256866	PHLDB3	cis	cerebellum	SCAN
rs7256866	ZFP36	cis	parietal	SCAN
rs7256866	SERTAD3	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35761200-35772200	Weak transcription	Psoas Muscle	Psoas
2	chr19:35761400-35772000	Strong transcription	Fetal Stomach	stomach
3	chr19:35761400-35775600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:35761600-35771400	Strong transcription	Fetal Intestine Small	intestine
5	chr19:35761600-35771400	Strong transcription	Skeletal Muscle Female	skeletal muscle
6	chr19:35762400-35772000	Weak transcription	K562	blood
7	chr19:35762800-35772000	Weak transcription	Stomach Mucosa	stomach
8	chr19:35762800-35780000	Weak transcription	Hela-S3	cervix
9	chr19:35763200-35771800	Strong transcription	Fetal Muscle Leg	muscle
10	chr19:35763400-35771400	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr19:35763400-35771400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr19:35763600-35771600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr19:35763600-35772800	Weak transcription	HSMMtube	muscle
14	chr19:35763600-35773400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr19:35764400-35771400	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr19:35764400-35771400	Weak transcription	NHDF-Ad	bronchial
17	chr19:35765400-35772800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr19:35765800-35771400	Strong transcription	Placenta	Placenta
19	chr19:35767600-35771600	Weak transcription	Fetal Kidney	kidney
20	chr19:35767800-35772800	Weak transcription	Osteobl	bone
21	chr19:35767800-35775800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:35768000-35771400	Weak transcription	Brain Angular Gyrus	brain
23	chr19:35768200-35772200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:35768200-35775600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr19:35768400-35773400	Weak transcription	Small Intestine	intestine
26	chr19:35768400-35781400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:35768800-35771400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:35768800-35781400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:35769000-35772600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr19:35769200-35775600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:35769800-35775600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:35770000-35771600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr19:35770000-35772000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr19:35770000-35772800	Weak transcription	Primary T cells from cord blood	blood
35	chr19:35770000-35775600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr19:35770000-35775800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr19:35770200-35772000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:35770200-35772200	Weak transcription	Dnd41	blood
39	chr19:35770200-35772600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr19:35770200-35773000	Enhancers	HepG2	liver
41	chr19:35770200-35773000	Weak transcription	HMEC	breast
42	chr19:35770200-35775400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr19:35770200-35775600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr19:35770400-35771600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr19:35770400-35772000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr19:35770400-35772000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr19:35770400-35772000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr19:35770400-35772200	Weak transcription	Colonic Mucosa	Colon
49	chr19:35770400-35772400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr19:35770400-35776800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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