Variant report

Variant	rs12984160
Chromosome Location	chr19:41815713-41815714
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	chr19:41815708-41816733	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:41811701-41817543	SK-N-MC	brain:	n/a	n/a
3	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
4	TCF12	chr19:41815431-41816827	A549	lung:	n/a	n/a
5	HEY1	chr19:41815706-41816661	HepG2	liver:	n/a	chr19:41816091-41816106 chr19:41816175-41816190
6	POLR2A	chr19:41813221-41816825	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:41813405-41816912	HepG2	liver:	n/a	n/a
8	POLR2A	chr19:41813668-41816626	GM18505	blood:	n/a	n/a
9	POLR2A	chr19:41815611-41816818	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr19:41814046-41816774	PBDE	blood:	n/a	n/a
11	POLR2A	chr19:41813712-41816830	GM12891	blood:	n/a	n/a
12	CHD2	chr19:41815534-41816478	K562	blood:	n/a	n/a
13	POLR2A	chr19:41815694-41816802	K562	blood:	n/a	n/a
14	POLR2A	chr19:41814998-41815716	H1-hESC	embryonic stem cell:	n/a	n/a
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	TAF1	chr19:41815356-41816775	A549	lung:	n/a	n/a
19	PML	chr19:41815647-41816566	K562	blood:	n/a	chr19:41816305-41816313
20	SIX5	chr19:41814064-41817340	A549	lung:	n/a	n/a
21	USF1	chr19:41814309-41816830	A549	lung:	n/a	n/a
22	SIN3AK20	chr19:41814155-41816958	A549	lung:	n/a	n/a
23	SIN3AK20	chr19:41815011-41816852	MCF-7	breast:	n/a	n/a
24	POLR2A	chr19:41812504-41817492	U87	brain:	n/a	n/a
25	STAT5A	chr19:41815173-41816650	GM12878	blood:	n/a	chr19:41816016-41816024
26	MAX	chr19:41813797-41817106	A549	lung:	n/a	n/a
27	POLR2A	chr19:41813633-41816880	GM12892	blood:	n/a	n/a
28	BCL3	chr19:41815100-41816882	K562	blood:	n/a	chr19:41815872-41815881
29	POLR2A	chr19:41813724-41815833	HL-60	blood:	n/a	n/a
30	POLR2A	chr19:41813664-41816817	PFSK-1	brain:	n/a	n/a
31	POLR2A	chr19:41813202-41816983	A549	lung:	n/a	n/a
32	PML	chr19:41815578-41816657	K562	blood:	n/a	chr19:41816305-41816313
33	ZMIZ1	chr19:41815694-41816539	K562	blood:	n/a	n/a
34	POLR2A	chr19:41813044-41816956	K562	blood:	n/a	n/a
35	BCLAF1	chr19:41815645-41816578	GM12878	blood:	n/a	chr19:41815872-41815881
36	EP300	chr19:41813969-41817062	A549	lung:	n/a	chr19:41814884-41814894 chr19:41816284-41816300 chr19:41816176-41816185
37	BCL3	chr19:41815212-41815772	GM12878	blood:	n/a	n/a
38	POLR2A	chr19:41813768-41817133	HUVEC	blood vessel:	n/a	n/a
39	GABPA	chr19:41815512-41816909	A549	lung:	n/a	chr19:41816277-41816286 chr19:41816051-41816060 chr19:41816049-41816060 chr19:41816049-41816063
40	POLR2A	chr19:41813358-41817263	SK-N-SH	brain:	n/a	n/a
41	BCLAF1	chr19:41815698-41816811	GM12878	blood:	n/a	chr19:41815872-41815881
42	ELF1	chr19:41814943-41816604	GM12878	blood:	n/a	chr19:41816025-41816037 chr19:41816175-41816187
43	POLR2A	chr19:41815628-41816556	GM12878	blood:	n/a	n/a
44	PBX3	chr19:41813734-41817130	A549	lung:	n/a	chr19:41815964-41815973
45	BCL3	chr19:41813653-41817132	A549	lung:	n/a	chr19:41815872-41815881 chr19:41814588-41814596
46	ELF1	chr19:41815337-41816587	SK-N-SH	brain:	n/a	chr19:41816025-41816037 chr19:41816175-41816187
47	POLR2A	chr19:41813847-41816723	PANC-1	pancreas:	n/a	n/a
48	NFATC1	chr19:41814007-41816542	GM12878	blood:	n/a	n/a
49	PBX3	chr19:41814294-41816911	A549	lung:	n/a	chr19:41815964-41815973
50	EP300	chr19:41814110-41816824	A549	lung:	n/a	chr19:41814884-41814894 chr19:41816284-41816300 chr19:41816176-41816185

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	chr19:41814701..41816825-chr19:41855352..41857612,2	K562	blood:
7	chr19:41813131..41816938-chr19:41856231..41860417,4	MCF-7	breast:
8	chr19:41813982..41818537-chr19:41824784..41829010,7	MCF-7	breast:
9	chr19:41767589..41772847-chr19:41812402..41817981,15	MCF-7	breast:
10	chr19:41814452..41815994-chr19:41869438..41871305,2	K562	blood:
11	chr19:41766631..41773289-chr19:41812153..41817614,9	K562	blood:
12	chr19:41814729..41817632-chr19:41858391..41861046,3	K562	blood:
13	chr19:41814514..41817967-chr19:41856512..41859507,4	MCF-7	breast:
14	chr19:41814494..41816860-chr19:41868645..41871305,2	K562	blood:

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

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10410836	0.92[EUR][1000 genomes]
rs10421990	0.91[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs1056854	1.00[ASW][hapmap];0.91[CEU][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11466345	0.81[JPT][hapmap]
rs11466347	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11466359	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11879429	0.87[ASN][1000 genomes]
rs11879435	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11879562	0.91[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs11880564	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11880729	0.87[ASN][1000 genomes]
rs11881940	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11881953	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12327659	0.91[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs12972266	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12972949	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12974323	0.92[EUR][1000 genomes]
rs12974420	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12976536	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12977563	0.87[ASN][1000 genomes]
rs12980267	0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs12980298	0.81[EUR][1000 genomes]
rs12980480	0.91[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs12980942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12981053	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12983047	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12983339	0.89[ASN][1000 genomes]
rs12985162	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12985339	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16958994	0.95[EUR][1000 genomes]
rs16958996	0.95[EUR][1000 genomes]
rs16958999	0.95[EUR][1000 genomes]
rs1865051	1.00[CEU][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs1865052	0.95[EUR][1000 genomes]
rs1865053	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs1946612	0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1946613	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2053086	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241718	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2241719	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2241720	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304230	0.91[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs2304231	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2304232	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34075897	0.92[EUR][1000 genomes]
rs34322801	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34772093	0.81[ASN][1000 genomes]
rs34945449	0.95[EUR][1000 genomes]
rs35501756	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35546772	0.82[ASN][1000 genomes]
rs35812313	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3745295	0.91[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs3752705	0.91[CEU][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs3760659	0.94[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs3760660	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816052	0.91[CEU][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs3826714	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4456618	1.00[CEU][hapmap];0.80[CHB][hapmap];0.98[EUR][1000 genomes]
rs4591267	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61459202	0.98[ASN][1000 genomes]
rs66724427	0.92[EUR][1000 genomes]
rs67511749	0.95[EUR][1000 genomes]
rs67744888	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6957	1.00[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs7245398	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs7248164	0.91[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs7250883	0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs7254679	0.82[CEU][hapmap]
rs7256416	0.92[EUR][1000 genomes]
rs7256856	0.92[EUR][1000 genomes]
rs7257310	1.00[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs7257742	0.92[EUR][1000 genomes]
rs7257825	0.92[EUR][1000 genomes]
rs7258749	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs8103839	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8105161	1.00[CEU][hapmap]
rs8105901	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8109167	1.00[CEU][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12984160	PLEKHA4	cis	cerebellum	SCAN
rs12984160	FLT3LG	cis	cerebellum	SCAN
rs12984160	TSKS	cis	parietal	SCAN
rs12984160	BAX	cis	cerebellum	SCAN

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	chr19:41812400-41815800	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr19:41812400-41815800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:41812600-41815800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:41812600-41815800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr19:41812800-41816000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:41813000-41815800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
8	chr19:41813000-41815800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr19:41813000-41816000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
10	chr19:41813200-41816000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr19:41813200-41816000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:41813400-41816000	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr19:41814200-41815800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:41814400-41817400	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr19:41814600-41815800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr19:41814600-41815800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr19:41814600-41815800	Flanking Active TSS	Brain Germinal Matrix	brain
18	chr19:41814600-41815800	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr19:41814600-41815800	Flanking Active TSS	Fetal Brain Male	brain
20	chr19:41814600-41816000	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr19:41814600-41816000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr19:41814800-41815800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr19:41814800-41815800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr19:41815000-41815800	Flanking Active TSS	Fetal Muscle Leg	muscle
25	chr19:41815000-41815800	Flanking Active TSS	Osteobl	bone
26	chr19:41815200-41815800	Flanking Active TSS	Fetal Thymus	thymus
27	chr19:41815200-41817000	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr19:41815200-41817000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:41815200-41817000	Active TSS	Esophagus	oesophagus
30	chr19:41815200-41817000	Active TSS	Ovary	ovary
31	chr19:41815200-41817200	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr19:41815200-41817200	Active TSS	Right Ventricle	heart
33	chr19:41815200-41817400	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr19:41815200-41817600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:41815200-41817800	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr19:41815400-41815800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr19:41815400-41815800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr19:41815400-41815800	Flanking Active TSS	Fetal Heart	heart
39	chr19:41815400-41815800	Flanking Active TSS	Fetal Muscle Trunk	muscle
40	chr19:41815400-41815800	Active TSS	HepG2	liver
41	chr19:41815400-41816600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr19:41815400-41816600	Active TSS	Brain Anterior Caudate	brain
43	chr19:41815400-41816600	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr19:41815400-41816600	Active TSS	Duodenum Mucosa	Duodenum
45	chr19:41815400-41816600	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr19:41815400-41816600	Active TSS	Lung	lung
47	chr19:41815400-41816600	Active TSS	Pancreas	Pancrea
48	chr19:41815400-41816600	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr19:41815400-41816600	Active TSS	NH-A	brain
50	chr19:41815400-41816800	Active TSS	Breast Myoepithelial Primary Cells	Breast

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