Variant report

Variant	rs2871921
Chromosome Location	chr19:36232420-36232421
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	chr19:36227527-36232589	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:36230963-36232726	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:36229905-36232561	GM19193	blood:	n/a	n/a
4	POLR2A	chr19:36227197-36234067	GM12891	blood:	n/a	n/a
5	POLR2A	chr19:36230150-36232463	K562	blood:	n/a	n/a
6	SIX5	chr19:36230618-36232431	A549	lung:	n/a	n/a
7	POLR2A	chr19:36232403-36232794	GM12891	blood:	n/a	n/a
8	MAZ	chr19:36231037-36232458	IMR90	lung:	n/a	n/a
9	CEBPD	chr19:36231165-36232519	K562	blood:	n/a	n/a
10	GATA2	chr19:36231958-36232430	K562	blood:	n/a	chr19:36232091-36232100
11	POLR2A	chr19:36227116-36234243	GM12878	blood:	n/a	n/a
12	CEBPD	chr19:36232014-36232496	K562	blood:	n/a	n/a
13	MXI1	chr19:36230397-36232481	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr19:36228209-36234132	GM12878	blood:	n/a	n/a
15	TCF12	chr19:36229327-36232727	A549	lung:	n/a	chr19:36230550-36230557
16	POLR2A	chr19:36228568-36232659	HepG2	liver:	n/a	n/a
17	TAL1	chr19:36231296-36232465	K562	blood:	n/a	chr19:36232082-36232100
18	POLR2A	chr19:36228270-36232672	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36205476..36213390-chr19:36226310..36233646,27	MCF-7	breast:
2	chr19:36231491..36233720-chr19:36248400..36250494,2	MCF-7	breast:
3	chr19:36231818..36233362-chr19:36425701..36428426,2	MCF-7	breast:

Variant related genes	Relation type
PSENEN	TF binding region
IGFLR1	TF binding region
ENSG00000188223	TF binding region
ENSG00000272333	Chromatin interaction
ENSG00000004776	Chromatin interaction
ENSG00000167595	Chromatin interaction
ENSG00000126243	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10401156	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10402601	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10402837	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10413852	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs11549030	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12459634	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12461285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12461333	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs12463059	0.93[ASN][1000 genomes]
rs2234371	0.93[ASN][1000 genomes]
rs2239947	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2291067	0.80[MEX][hapmap]
rs2293686	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28633929	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs28656784	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34031911	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs35209304	0.81[ASN][1000 genomes]
rs35729071	0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs3746277	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3761087	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3848662	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56189160	0.81[ASN][1000 genomes]
rs62109452	0.90[ASN][1000 genomes]
rs62112162	0.85[EUR][1000 genomes]
rs7249885	0.90[ASN][1000 genomes]
rs7254601	0.82[JPT][hapmap]
rs7260184	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73048504	0.90[ASN][1000 genomes]
rs8106959	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];1.00[ASN][1000 genomes]
rs9304874	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv911633	chr19:36206050-36283847	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911634	chr19:36206050-36290977	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
9	nsv543996	chr19:36210269-36265431	Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1057830	chr19:36210269-36279794	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv543997	chr19:36210269-36279794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
12	nsv911635	chr19:36217333-36283847	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv515536	chr19:36219525-36240960	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
14	nsv458567	chr19:36221051-36283847	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
15	nsv579423	chr19:36221051-36283847	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs2871921	TMEM149	cis	multi-tissue	Pritchard
rs2871921	TMEM149	cis	Brain Pons	GTEx
rs2871921	UPK1A	trans	cerebellum	SCAN
rs2871921	TMEM149	Cis_1M	lymphoblastoid	RTeQTL
rs2871921	TMEM149	cis	Liver	GTEx
rs2871921	TMEM149	cis	lymphoblastoid	seeQTL
rs2871921	U2AF1L4	cis	Esophagus Muscularis	GTEx
rs2871921	U2AF1L4	Cis_1M	lymphoblastoid	RTeQTL
rs2871921	ZNF568	cis	cerebellum	SCAN
rs2871921	U2AF1L4	cis	lung	GTEx
rs2871921	U2AF1L4	cis	Whole Blood	GTEx
rs2871921	U2AF1L4	cis	Muscle Skeletal	GTEx
rs2871921	U2AF1L4	cis	multi-tissue	Pritchard
rs2871921	TMEM149	cis	normal skin	skin_eQTL
rs2871921	U2AF1L4	cis	Liver	GTEx
rs2871921	LIN37	Cis_1M	lymphoblastoid	RTeQTL
rs2871921	PSG1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36230600-36232600	Active TSS	H9 Cell Line	embryonic stem cell
2	chr19:36230600-36232600	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr19:36230600-36232600	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr19:36230600-36232600	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr19:36230600-36232800	Flanking Active TSS	Dnd41	blood
6	chr19:36230600-36233200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr19:36230800-36233000	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr19:36230800-36234000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr19:36230800-36234000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
10	chr19:36230800-36234000	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr19:36230800-36234000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:36230800-36234000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:36230800-36234200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr19:36230800-36234400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr19:36231000-36232600	Active TSS	H1 Cell Line	embryonic stem cell
16	chr19:36231000-36232600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:36231000-36232600	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr19:36231000-36232600	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr19:36231000-36232600	Flanking Active TSS	Fetal Thymus	thymus
20	chr19:36231000-36232600	Active TSS	HepG2	liver
21	chr19:36231000-36232800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:36231000-36233200	Active TSS	Rectal Smooth Muscle	rectum
23	chr19:36231000-36234000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr19:36231200-36232600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr19:36231200-36232600	Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr19:36231200-36232600	Active TSS	GM12878-XiMat	blood
27	chr19:36231200-36232600	Active TSS	K562	blood
28	chr19:36231200-36232800	Active TSS	Thymus	Thymus
29	chr19:36231200-36233000	Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr19:36231200-36233800	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr19:36231400-36232600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr19:36231400-36232600	Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr19:36231400-36232600	Active TSS	Brain Germinal Matrix	brain
34	chr19:36231400-36235200	Weak transcription	Fetal Heart	heart
35	chr19:36231800-36234000	Flanking Active TSS	Primary B cells from peripheral blood	blood
36	chr19:36231800-36234000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:36231800-36234200	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr19:36232000-36234800	Weak transcription	Gastric	stomach
39	chr19:36232200-36232600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr19:36232200-36232600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr19:36232200-36232600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:36232200-36232600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr19:36232200-36232600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr19:36232200-36232600	Active TSS	HSMMtube	muscle
45	chr19:36232200-36232800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:36232200-36232800	Weak transcription	Fetal Intestine Small	intestine
47	chr19:36232200-36233000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr19:36232200-36233000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr19:36232200-36233000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:36232200-36233000	Weak transcription	Brain Hippocampus Middle	brain

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