Variant report

Variant	rs2241713
Chromosome Location	chr19:41869468-41869469
allele	C/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	chr19:41869445-41870895	K562	blood:	n/a	n/a
2	HEY1	chr19:41869459-41870726	K562	blood:	n/a	n/a
3	POLR2A	chr19:41869436-41870451	Raji	blood:	n/a	n/a
4	RELA	chr19:41869460-41870858	GM18505	blood:	n/a	chr19:41869689-41869698 chr19:41870397-41870406 chr19:41870397-41870406 chr19:41869689-41869698
5	YY1	chr19:41869344-41871111	A549	lung:	n/a	chr19:41870237-41870259 chr19:41870211-41870221 chr19:41870214-41870222 chr19:41870164-41870180 chr19:41870236-41870248 chr19:41870240-41870248 chr19:41870237-41870247 chr19:41870127-41870136 chr19:41870210-41870222 chr19:41870211-41870221 chr19:41870235-41870254 chr19:41870211-41870233
6	POLR2A	chr19:41869446-41870662	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr19:41869428-41870866	GM12891	blood:	n/a	n/a
8	RCOR1	chr19:41869372-41870811	GM12878	blood:	n/a	n/a
9	TEAD4	chr19:41869320-41870795	K562	blood:	n/a	n/a
10	POLR2A	chr19:41869466-41870906	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr19:41869425-41870678	K562	blood:	n/a	n/a
12	MYBL2	chr19:41869405-41870552	HepG2	liver:	n/a	chr19:41869873-41869883
13	RELA	chr19:41869310-41870686	GM12891	blood:	n/a	chr19:41869689-41869698 chr19:41870397-41870406 chr19:41870397-41870406 chr19:41869689-41869698
14	POLR2A	chr19:41869456-41871146	MCF10A-Er-Src	breast:	n/a	n/a
15	RELA	chr19:41869257-41870754	GM15510	blood:	n/a	chr19:41869689-41869698 chr19:41870397-41870406 chr19:41870397-41870406 chr19:41869689-41869698
16	POLR2A	chr19:41869301-41871160	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr19:41869433-41870507	GM15510	blood:	n/a	n/a
18	TCF12	chr19:41869359-41870626	A549	lung:	n/a	n/a
19	BHLHE40	chr19:41869223-41870567	GM12878	blood:	n/a	n/a
20	ELF1	chr19:41869214-41870835	A549	lung:	n/a	chr19:41870124-41870136
21	GABPA	chr19:41869381-41870787	A549	lung:	n/a	chr19:41869942-41869951 chr19:41870127-41870136 chr19:41869843-41869854 chr19:41869794-41869803 chr19:41869843-41869852 chr19:41869794-41869805 chr19:41869840-41869854
22	MTA3	chr19:41868956-41871022	GM12878	blood:	n/a	n/a
23	PBX3	chr19:41869191-41871124	A549	lung:	n/a	n/a
24	MAX	chr19:41869392-41870948	A549	lung:	n/a	n/a
25	RELA	chr19:41869321-41870815	GM10847	blood:	n/a	chr19:41869689-41869698 chr19:41870397-41870406 chr19:41870397-41870406 chr19:41869689-41869698
26	MAX	chr19:41869267-41870637	GM12878	blood:	n/a	n/a
27	POLR2A	chr19:41869386-41870584	MCF10A-Er-Src	breast:	n/a	n/a
28	ATF3	chr19:41869231-41870758	A549	lung:	n/a	chr19:41870127-41870136
29	PBX3	chr19:41869338-41870435	A549	lung:	n/a	n/a
30	POLR2A	chr19:41869299-41870743	U87	brain:	n/a	n/a
31	POLR2A	chr19:41869454-41870719	PFSK-1	brain:	n/a	n/a
32	RELA	chr19:41869308-41870697	GM19099	blood:	n/a	chr19:41869689-41869698 chr19:41870397-41870406 chr19:41870397-41870406 chr19:41869689-41869698
33	POLR2A	chr19:41869414-41870753	U87	brain:	n/a	n/a
34	REST	chr19:41869386-41870803	H1-neurons	neurons:	n/a	chr19:41870346-41870366
35	POLR2A	chr19:41869411-41870542	GM12878	blood:	n/a	n/a
36	REST	chr19:41869416-41870796	A549	lung:	n/a	chr19:41870346-41870366
37	POLR2A	chr19:41869452-41870446	GM12878	blood:	n/a	n/a
38	CREB1	chr19:41869459-41870515	A549	lung:	n/a	n/a
39	NRF1	chr19:41869357-41870694	SK-N-SH	brain:	n/a	chr19:41869942-41869951 chr19:41870127-41870136 chr19:41869793-41869804 chr19:41869843-41869854 chr19:41869794-41869803 chr19:41869843-41869852 chr19:41869794-41869805 chr19:41869840-41869854
40	YY1	chr19:41869120-41870675	GM12878	blood:	n/a	chr19:41870237-41870259 chr19:41870211-41870221 chr19:41870214-41870222 chr19:41870164-41870180 chr19:41870236-41870248 chr19:41870240-41870248 chr19:41870237-41870247 chr19:41870127-41870136 chr19:41870210-41870222 chr19:41870211-41870221 chr19:41870235-41870254 chr19:41870211-41870233
41	POLR2A	chr19:41868972-41871020	GM12878	blood:	n/a	n/a
42	YY1	chr19:41869445-41870899	K562	blood:	n/a	chr19:41870237-41870259 chr19:41870211-41870221 chr19:41870214-41870222 chr19:41870164-41870180 chr19:41870236-41870248 chr19:41870240-41870248 chr19:41870237-41870247 chr19:41870127-41870136 chr19:41870210-41870222 chr19:41870211-41870221 chr19:41870235-41870254 chr19:41870211-41870233
43	HEY1	chr19:41869378-41870531	HepG2	liver:	n/a	n/a
44	POLR2A	chr19:41869436-41870756	K562	blood:	n/a	n/a
45	BCL3	chr19:41869300-41871014	A549	lung:	n/a	chr19:41870397-41870406 chr19:41870161-41870170
46	POLR2A	chr19:41869166-41870753	GM12878	blood:	n/a	n/a
47	TBP	chr19:41869395-41870725	GM12878	blood:	n/a	n/a
48	EP300	chr19:41869319-41870672	A549	lung:	n/a	chr19:41870570-41870579 chr19:41870648-41870662 chr19:41869942-41869951
49	GABPA	chr19:41869412-41870695	MCF-7	breast:	n/a	chr19:41869942-41869951 chr19:41870127-41870136 chr19:41869843-41869854 chr19:41869794-41869803 chr19:41869843-41869852 chr19:41869794-41869805 chr19:41869840-41869854
50	POLR2A	chr19:41869029-41870764	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41856910..41863042-chr19:41867113..41873191,18	MCF-7	breast:
2	chr19:41868160..41870059-chr19:41902135..41903854,4	K562	blood:
3	chr19:41858489..41863412-chr19:41867730..41871601,11	K562	blood:
4	chr19:41868161..41871707-chr19:41902716..41905358,4	MCF-7	breast:
5	chr19:41868336..41871272-chr19:41944233..41948538,5	K562	blood:
6	chr19:41824554..41827469-chr19:41868894..41871689,2	K562	blood:
7	chr19:41855697..41857432-chr19:41868390..41870729,2	K562	blood:
8	chr19:41868160..41871597-chr19:41899998..41904284,10	K562	blood:
9	chr19:41868336..41870018-chr19:41944233..41946275,2	K562	blood:
10	chr19:41814494..41816860-chr19:41868645..41871305,2	K562	blood:
11	chr14:56046261..56047012-chr19:41869306..41870109,2	NB4	blood:

Variant related genes	Relation type
TMEM91	TF binding region
ENSG00000077348	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000255730	Chromatin interaction
ENSG00000268987	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000142039	Chromatin interaction
ENSG00000126777	Chromatin interaction
ENSG00000248098	Chromatin interaction
ENSG00000186615	Chromatin interaction
ENSG00000105341	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1025497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1046909	0.81[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs11083616	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083617	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666933	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11670143	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11670739	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12462166	0.97[ASN][1000 genomes]
rs12983775	0.92[ASN][1000 genomes]
rs1549933	0.98[ASN][1000 genomes]
rs1800469	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1800470	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1963413	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1982072	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2241712	0.99[ASN][1000 genomes]
rs2241714	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2241715	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2317130	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34503210	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4803457	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803458	0.90[ASN][1000 genomes]
rs4803459	0.87[ASN][1000 genomes]
rs7260340	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8108357	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9797885	0.97[ASN][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	nsv521311	chr19:41856886-41882712	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2241713	B3GALT7	cis	multi-tissue	Pritchard
rs2241713	LHB	cis	parietal	SCAN
rs2241713	MGC4093	cis	multi-tissue	Pritchard
rs2241713	CCDC114	cis	parietal	SCAN
rs2241713	PSG2	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41868200-41869800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr19:41868200-41869800	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr19:41868600-41869600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
4	chr19:41868800-41869600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
5	chr19:41868800-41869600	Flanking Active TSS	Dnd41	blood
6	chr19:41868800-41869600	Flanking Active TSS	GM12878-XiMat	blood
7	chr19:41869000-41869600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:41869000-41869600	Flanking Active TSS	Brain Angular Gyrus	brain
9	chr19:41869000-41869600	Flanking Active TSS	Colonic Mucosa	Colon
10	chr19:41869000-41869600	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr19:41869000-41869600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr19:41869000-41869600	Enhancers	Small Intestine	intestine
13	chr19:41869000-41869600	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr19:41869000-41869600	Enhancers	Spleen	Spleen
15	chr19:41869000-41869600	Flanking Active TSS	K562	blood
16	chr19:41869000-41869600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr19:41869000-41869800	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr19:41869000-41869800	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr19:41869000-41869800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr19:41869000-41869800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:41869000-41869800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:41869000-41869800	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr19:41869000-41870600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:41869200-41869600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr19:41869200-41869600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr19:41869200-41869600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:41869200-41869600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr19:41869200-41869600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:41869200-41869600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr19:41869200-41869600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr19:41869200-41869600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:41869200-41869600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:41869200-41869600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr19:41869200-41869600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr19:41869200-41869600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr19:41869200-41869600	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr19:41869200-41869600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr19:41869200-41869600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr19:41869200-41869600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr19:41869200-41869600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr19:41869200-41869600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr19:41869200-41869600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr19:41869200-41869600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:41869200-41869600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr19:41869200-41869600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr19:41869200-41869600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:41869200-41869600	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr19:41869200-41869600	Flanking Active TSS	Brain Cingulate Gyrus	brain
49	chr19:41869200-41869600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
50	chr19:41869200-41869600	Flanking Active TSS	Colon Smooth Muscle	Colon

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