Variant report

Variant	rs2217656
Chromosome Location	chr19:41814897-41814898
allele	G/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	POLR2A	chr19:41811701-41817543	SK-N-MC	brain:	n/a	n/a
2	CTCF	chr19:41811702-41817527	A549	lung:	n/a	chr19:41814589-41814607 chr19:41814590-41814606 chr19:41814584-41814605 chr19:41814591-41814604 chr19:41814591-41814604 chr19:41813852-41813873 chr19:41813850-41813868 chr19:41814601-41814614
3	MBD4	chr19:41814198-41814924	HepG2	liver:	n/a	n/a
4	SMC3	chr19:41813494-41815570	SK-N-SH	brain:	n/a	chr19:41814591-41814605
5	RAD21	chr19:41814227-41814914	HCT-116	colon:	n/a	chr19:41814587-41814606 chr19:41814589-41814601 chr19:41814600-41814613 chr19:41814597-41814616 chr19:41814591-41814605
6	WRNIP1	chr19:41814273-41815305	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:41813221-41816825	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:41813405-41816912	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:41813668-41816626	GM18505	blood:	n/a	n/a
10	POLR2A	chr19:41814046-41816774	PBDE	blood:	n/a	n/a
11	TEAD4	chr19:41814134-41814940	K562	blood:	n/a	n/a
12	POLR2A	chr19:41813712-41816830	GM12891	blood:	n/a	n/a
13	POLR2A	chr19:41813813-41815574	GM12891	blood:	n/a	n/a
14	RELA	chr19:41814218-41815031	GM12878	blood:	n/a	chr19:41814551-41814560 chr19:41814551-41814560
15	STAT5A	chr19:41813753-41816690	GM12878	blood:	n/a	chr19:41814315-41814323 chr19:41813977-41813985 chr19:41816016-41816024
16	POLR2A	chr19:41809524-41818013	K562	blood:	n/a	n/a
17	POLR2A	chr19:41813354-41817333	K562	blood:	n/a	n/a
18	FOXM1	chr19:41814140-41814943	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:41814139-41814898	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZMIZ1	chr19:41814393-41814955	K562	blood:	n/a	n/a
21	CTCF	chr19:41814840-41814990	K562	blood:	n/a	n/a
22	HCFC1	chr19:41814435-41814911	K562	blood:	n/a	n/a
23	RCOR1	chr19:41814165-41815010	GM12878	blood:	n/a	n/a
24	ZBTB33	chr19:41814380-41815435	A549	lung:	n/a	n/a
25	SIX5	chr19:41814064-41817340	A549	lung:	n/a	n/a
26	USF1	chr19:41814309-41816830	A549	lung:	n/a	n/a
27	SIN3AK20	chr19:41814155-41816958	A549	lung:	n/a	n/a
28	CTCF	chr19:41814317-41814911	K562	blood:	n/a	chr19:41814589-41814607 chr19:41814590-41814606 chr19:41814584-41814605 chr19:41814591-41814604 chr19:41814591-41814604 chr19:41814601-41814614
29	BCL3	chr19:41813942-41815083	K562	blood:	n/a	chr19:41814588-41814596
30	ELF1	chr19:41814232-41814923	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:41814411-41814978	ProgFib	skin:	n/a	n/a
32	CTCF	chr19:41814151-41814956	GM12878	blood:	n/a	chr19:41814589-41814607 chr19:41814590-41814606 chr19:41814584-41814605 chr19:41814591-41814604 chr19:41814591-41814604 chr19:41814601-41814614
33	POLR2A	chr19:41812504-41817492	U87	brain:	n/a	n/a
34	MAX	chr19:41813797-41817106	A549	lung:	n/a	n/a
35	POLR2A	chr19:41813633-41816880	GM12892	blood:	n/a	n/a
36	RUNX3	chr19:41814152-41815592	GM12878	blood:	n/a	n/a
37	POLR2A	chr19:41813724-41815833	HL-60	blood:	n/a	n/a
38	POLR2A	chr19:41813664-41816817	PFSK-1	brain:	n/a	n/a
39	POLR2A	chr19:41813202-41816983	A549	lung:	n/a	n/a
40	FOXA2	chr19:41814345-41815079	A549	lung:	n/a	chr19:41814881-41814893
41	POLR2A	chr19:41813044-41816956	K562	blood:	n/a	n/a
42	EP300	chr19:41813969-41817062	A549	lung:	n/a	chr19:41814884-41814894 chr19:41816284-41816300 chr19:41816176-41816185
43	POLR2A	chr19:41812949-41815614	K562	blood:	n/a	n/a
44	POLR2A	chr19:41813768-41817133	HUVEC	blood vessel:	n/a	n/a
45	POLR2A	chr19:41813358-41817263	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr19:41813811-41814918	A549	lung:	n/a	n/a
47	PBX3	chr19:41813734-41817130	A549	lung:	n/a	chr19:41815964-41815973
48	BCL3	chr19:41813653-41817132	A549	lung:	n/a	chr19:41815872-41815881 chr19:41814588-41814596
49	POLR2A	chr19:41813847-41816723	PANC-1	pancreas:	n/a	n/a
50	NFATC1	chr19:41814007-41816542	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41799355..41806261-chr19:41812914..41817863,9	MCF-7	breast:
2	chr19:41808201..41810426-chr19:41812838..41816052,5	K562	blood:
3	chr19:41814451..41817514-chr19:41857748..41860161,3	K562	blood:
4	chr19:41768451..41772660-chr19:41814640..41817683,6	MCF-7	breast:
5	chr19:41766963..41771332-chr19:41813075..41817628,7	K562	blood:
6	chr19:41709903..41710828-chr19:41814558..41815062,3	K562	blood:
7	chr19:41711943..41714623-chr19:41813301..41815470,3	MCF-7	breast:
8	chr19:41814701..41816825-chr19:41855352..41857612,2	K562	blood:
9	chr19:41813131..41816938-chr19:41856231..41860417,4	MCF-7	breast:
10	chr19:41813982..41818537-chr19:41824784..41829010,7	MCF-7	breast:
11	chr19:41709937..41710810-chr19:41814166..41815131,2	MCF-7	breast:
12	chr19:41767589..41772847-chr19:41812402..41817981,15	MCF-7	breast:
13	chr19:41814452..41815994-chr19:41869438..41871305,2	K562	blood:
14	chr19:41766631..41773289-chr19:41812153..41817614,9	K562	blood:
15	chr19:41814729..41817632-chr19:41858391..41861046,3	K562	blood:
16	chr19:41814514..41817967-chr19:41856512..41859507,4	MCF-7	breast:
17	chr19:41814494..41816860-chr19:41868645..41871305,2	K562	blood:

Variant related genes	Relation type
CCDC97	TF binding region
ENSG00000255730	Chromatin interaction
ENSG00000123810	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000142039	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10414612	1.00[TSI][hapmap]
rs1051008	1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11466349	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16959007	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16975124	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16975156	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16975164	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1968453	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2288875	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810173	0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61247776	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246896	0.82[CHB][hapmap]
rs7249554	1.00[TSI][hapmap]
rs747857	1.00[CHB][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9304592	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs998468	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv17637	chr19:41770228-41815282	Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv911769	chr19:41813676-41845801	Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 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	chr19:41780200-41815800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:41788600-41815400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:41812400-41815800	Flanking Active TSS	Primary T cells from cord blood	blood
4	chr19:41812400-41815800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
5	chr19:41812600-41815000	Genic enhancers	A549	lung
6	chr19:41812600-41815200	Weak transcription	Ovary	ovary
7	chr19:41812600-41815600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
8	chr19:41812600-41815600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr19:41812600-41815800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:41812600-41815800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr19:41812800-41815000	Weak transcription	Aorta	Aorta
12	chr19:41812800-41815400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:41812800-41815400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr19:41812800-41815600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr19:41812800-41816000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:41813000-41815200	Enhancers	HUVEC	blood vessel
17	chr19:41813000-41815800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr19:41813000-41815800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr19:41813000-41816000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
20	chr19:41813200-41815400	Enhancers	Small Intestine	intestine
21	chr19:41813200-41815600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chr19:41813200-41815600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr19:41813200-41816000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr19:41813200-41816000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:41813400-41815200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:41813400-41816000	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr19:41813800-41815000	Enhancers	Pancreas	Pancrea
28	chr19:41813800-41815200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:41813800-41815200	Enhancers	Stomach Mucosa	stomach
30	chr19:41813800-41815200	Transcr. at gene 5' and 3'	Dnd41	blood
31	chr19:41814000-41815000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:41814000-41815000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:41814000-41815200	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr19:41814000-41815200	Enhancers	Psoas Muscle	Psoas
35	chr19:41814000-41815200	Enhancers	Right Atrium	heart
36	chr19:41814000-41815600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr19:41814200-41815000	Genic enhancers	Fetal Intestine Small	intestine
38	chr19:41814200-41815000	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr19:41814200-41815000	Enhancers	Hela-S3	cervix
40	chr19:41814200-41815200	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr19:41814200-41815200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:41814200-41815200	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr19:41814200-41815200	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr19:41814200-41815200	Enhancers	Primary B cells from peripheral blood	blood
45	chr19:41814200-41815200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr19:41814200-41815200	Enhancers	Liver	Liver
47	chr19:41814200-41815200	Enhancers	Right Ventricle	heart
48	chr19:41814200-41815200	Enhancers	HepG2	liver
49	chr19:41814200-41815400	Enhancers	H1 Cell Line	embryonic stem cell
50	chr19:41814200-41815400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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