Variant report

Variant	rs10402601
Chromosome Location	chr19:36236909-36236910
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	MAX	chr19:36235184-36237068	A549	lung:	n/a	chr19:36235447-36235457 chr19:36236419-36236435
2	JUND	chr19:36235525-36237044	A549	lung:	n/a	chr19:36236599-36236607
3	MXI1	chr19:36235293-36237237	IMR90	lung:	n/a	n/a
4	POLR2A	chr19:36235577-36236916	U87	brain:	n/a	n/a
5	FOSL2	chr19:36235499-36237055	A549	lung:	n/a	chr19:36236599-36236607
6	SP1	chr19:36235305-36236936	A549	lung:	n/a	chr19:36235611-36235620 chr19:36235626-36235640 chr19:36235610-36235619 chr19:36235667-36235681 chr19:36235609-36235621 chr19:36236173-36236182 chr19:36235610-36235620 chr19:36235449-36235458 chr19:36236735-36236744 chr19:36236734-36236744 chr19:36235611-36235620 chr19:36235608-36235615 chr19:36235610-36235620 chr19:36235609-36235621 chr19:36236671-36236680 chr19:36236734-36236744
7	ETS1	chr19:36235629-36236972	A549	lung:	n/a	chr19:36236352-36236365 chr19:36236332-36236339 chr19:36236353-36236366 chr19:36236583-36236590 chr19:36236330-36236339
8	POLR2A	chr19:36235790-36236926	Hela-S3	cervix:	n/a	n/a
9	EP300	chr19:36235739-36236910	K562	blood:	n/a	n/a
10	MAZ	chr19:36235328-36237351	IMR90	lung:	n/a	chr19:36235447-36235457 chr19:36236419-36236435
11	CREB1	chr19:36235449-36236963	A549	lung:	n/a	n/a
12	GABPA	chr19:36235536-36236953	MCF-7	breast:	n/a	chr19:36236473-36236482 chr19:36236473-36236484 chr19:36236411-36236422 chr19:36236470-36236484 chr19:36236413-36236422
13	ZBTB33	chr19:36235616-36237009	A549	lung:	n/a	n/a
14	EGR1	chr19:36235604-36236927	HCT-116	colon:	n/a	chr19:36236417-36236431 chr19:36236412-36236421 chr19:36236507-36236531 chr19:36236419-36236429 chr19:36236431-36236441 chr19:36236582-36236591 chr19:36236474-36236483
15	CEBPB	chr19:36236033-36237038	A549	lung:	n/a	n/a
16	BCL3	chr19:36235161-36237015	A549	lung:	n/a	chr19:36236330-36236339
17	TFAP2C	chr19:36235737-36236930	Hela-S3	cervix:	n/a	chr19:36236399-36236414
18	BCL3	chr19:36235409-36236984	A549	lung:	n/a	chr19:36236330-36236339
19	CHD1	chr19:36235309-36237067	IMR90	lung:	n/a	chr19:36235450-36235460
20	SIN3AK20	chr19:36235310-36236956	MCF-7	breast:	n/a	n/a
21	POLR2A	chr19:36235473-36236954	SK-N-MC	brain:	n/a	n/a
22	ELF1	chr19:36236200-36237160	K562	blood:	n/a	n/a
23	HCFC1	chr19:36235387-36237068	Hela-S3	cervix:	n/a	n/a
24	ZBTB7A	chr19:36236413-36236918	K562	blood:	n/a	chr19:36236606-36236617
25	ZBTB7A	chr19:36236230-36236912	K562	blood:	n/a	chr19:36236606-36236617
26	POLR2A	chr19:36235571-36236922	U87	brain:	n/a	n/a
27	SIN3A	chr19:36235510-36237128	H1-hESC	embryonic stem cell:	n/a	n/a
28	ELF1	chr19:36235514-36237065	MCF-7	breast:	n/a	n/a
29	SIX5	chr19:36235266-36237101	A549	lung:	n/a	chr19:36236353-36236362 chr19:36236355-36236364 chr19:36236352-36236366 chr19:36236506-36236520
30	GABPA	chr19:36235460-36237036	A549	lung:	n/a	chr19:36236473-36236482 chr19:36236473-36236484 chr19:36236411-36236422 chr19:36236470-36236484 chr19:36236413-36236422
31	TBL1XR1	chr19:36236759-36236943	K562	blood:	n/a	n/a
32	TAF1	chr19:36235433-36236911	H1-hESC	embryonic stem cell:	n/a	n/a
33	GABPA	chr19:36235561-36237261	A549	lung:	n/a	chr19:36236473-36236482 chr19:36236473-36236484 chr19:36236411-36236422 chr19:36236470-36236484 chr19:36236413-36236422
34	MXI1	chr19:36235282-36237124	SK-N-SH	brain:	n/a	n/a
35	REST	chr19:36235439-36237030	H1-neurons	neurons:	n/a	chr19:36235622-36235640
36	POLR2A	chr19:36235597-36236923	HUVEC	blood vessel:	n/a	n/a
37	ELF1	chr19:36234952-36237086	GM12878	blood:	n/a	n/a
38	TCF12	chr19:36235039-36237090	A549	lung:	n/a	chr19:36236151-36236161
39	NRF1	chr19:36235397-36237105	SK-N-SH	brain:	n/a	chr19:36235453-36235462 chr19:36236473-36236482 chr19:36236411-36236422 chr19:36236473-36236484 chr19:36236411-36236422 chr19:36236470-36236484 chr19:36236413-36236422
40	SIN3AK20	chr19:36235404-36237013	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36207379..36214815-chr19:36234227..36241330,25	MCF-7	breast:
2	chr19:36223134..36225733-chr19:36234939..36237543,2	MCF-7	breast:
3	chr19:35759096..35761188-chr19:36236088..36238876,2	MCF-7	breast:
4	chr19:36035683..36038067-chr19:36234353..36237102,3	K562	blood:
5	chr19:35643125..35645834-chr19:36235394..36237704,2	K562	blood:
6	chr19:36034766..36037168-chr19:36234979..36237516,2	MCF-7	breast:
7	chr19:36235922..36238148-chr19:36359346..36361404,2	MCF-7	breast:

Variant related genes	Relation type
IGFLR1	TF binding region
U2AF1L4	TF binding region
LIN37	TF binding region
ENSG00000267120	TF binding region
ENSG00000089327	Chromatin interaction
ENSG00000105698	Chromatin interaction
ENSG00000161270	Chromatin interaction
ENSG00000236144	Chromatin interaction
ENSG00000105677	Chromatin interaction
ENSG00000105663	Chromatin interaction
ENSG00000105290	Chromatin interaction
ENSG00000272333	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs10401156	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10402837	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11549030	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459634	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12461333	0.89[YRI][hapmap]
rs2239947	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28656784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871921	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34031911	0.82[AFR][1000 genomes]
rs3746277	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848662	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3848665	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62112162	0.87[EUR][1000 genomes]
rs7260184	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10402601	FLJ22573	cis	multi-tissue	Pritchard
rs10402601	U2AF1L4	cis	Esophagus Muscularis	GTEx
rs10402601	TMEM149	cis	normal skin	skin_eQTL
rs10402601	U2AF1L4	cis	Muscle Skeletal	GTEx
rs10402601	LIN37	Cis_1M	lymphoblastoid	RTeQTL
rs10402601	U2AF1L4	cis	multi-tissue	Pritchard
rs10402601	U2AF1L4	cis	Whole Blood	GTEx
rs10402601	TMEM149	cis	multi-tissue	Pritchard
rs10402601	TMEM149	Cis_1M	lymphoblastoid	RTeQTL
rs10402601	U2AF1L4	cis	lung	GTEx
rs10402601	U2AF1L4	Cis_1M	lymphoblastoid	RTeQTL
rs10402601	TMEM149	cis	Brain Pons	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36235000-36237200	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr19:36235000-36237800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr19:36235200-36237200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:36235200-36237200	Active TSS	H9 Cell Line	embryonic stem cell
5	chr19:36235200-36237200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:36235200-36237400	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr19:36235200-36237400	Active TSS	NHDF-Ad	bronchial
8	chr19:36235200-36237600	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr19:36235200-36238000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:36235400-36237200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:36235400-36237200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:36235400-36237600	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr19:36235600-36237000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr19:36235600-36237000	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr19:36235600-36237000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:36235600-36237000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:36235600-36237000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:36235600-36237000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr19:36235600-36237000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr19:36235600-36237000	Active TSS	Esophagus	oesophagus
21	chr19:36235600-36237000	Active TSS	Gastric	stomach
22	chr19:36235600-36237000	Active TSS	Placenta Amnion	Placenta Amnion
23	chr19:36235600-36237000	Active TSS	Right Atrium	heart
24	chr19:36235600-36237000	Active TSS	Small Intestine	intestine
25	chr19:36235600-36237000	Active TSS	Thymus	Thymus
26	chr19:36235600-36237000	Active TSS	GM12878-XiMat	blood
27	chr19:36235600-36237000	Active TSS	NH-A	brain
28	chr19:36235600-36237200	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr19:36235600-36237200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:36235600-36237200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:36235600-36237200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:36235600-36237200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:36235600-36237200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr19:36235600-36237200	Active TSS	Aorta	Aorta
35	chr19:36235600-36237200	Active TSS	Fetal Kidney	kidney
36	chr19:36235600-36237200	Active TSS	A549	lung
37	chr19:36235600-36237200	Active TSS	HMEC	breast
38	chr19:36235600-36237200	Active TSS	HSMM	muscle
39	chr19:36235600-36237400	Active TSS	Psoas Muscle	Psoas
40	chr19:36235800-36237000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr19:36235800-36237000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:36235800-36237000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr19:36235800-36237000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:36235800-36237000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:36235800-36237000	Active TSS	Brain Germinal Matrix	brain
46	chr19:36235800-36237000	Active TSS	Duodenum Mucosa	Duodenum
47	chr19:36235800-36237000	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr19:36235800-36237000	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr19:36235800-36237000	Active TSS	Left Ventricle	heart
50	chr19:36235800-36237000	Active TSS	Ovary	ovary

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