Variant report

Variant	rs3816959
Chromosome Location	chr5:40834864-40834865
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:270)
CpG islands
(count:0)
Chromatin interactive
region (count:42)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:270 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:40833886-40836321	GM12891	blood:	n/a	n/a
2	POLR2A	chr5:40824786-40836349	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr5:40833397-40836297	GM15510	blood:	n/a	n/a
4	MAZ	chr5:40834190-40836857	K562	blood:	n/a	n/a
5	RCOR1	chr5:40834861-40836655	K562	blood:	n/a	n/a
6	POLR2A	chr5:40833540-40836475	HL-60	blood:	n/a	n/a
7	GTF2F1	chr5:40834330-40836510	Hela-S3	cervix:	n/a	n/a
8	TBL1XR1	chr5:40834825-40835856	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:40830800-40836632	NB4	blood:	n/a	n/a
10	TAF1	chr5:40834831-40835817	GM12878	blood:	n/a	n/a
11	MYC	chr5:40833754-40836963	K562	blood:	n/a	n/a
12	POLR2A	chr5:40832709-40836399	GM18951	blood:	n/a	n/a
13	MAX	chr5:40834464-40836104	GM12878	blood:	n/a	n/a
14	RELA	chr5:40834498-40835751	GM19099	blood:	n/a	n/a
15	MAX	chr5:40834759-40836098	HCT-116	colon:	n/a	n/a
16	TAF1	chr5:40834808-40835973	H1-hESC	embryonic stem cell:	n/a	n/a
17	CHD2	chr5:40834004-40836006	K562	blood:	n/a	n/a
18	STAT5A	chr5:40834856-40835691	GM12878	blood:	n/a	n/a
19	POLR2A	chr5:40833813-40836384	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr5:40824383-40836719	K562	blood:	n/a	n/a
21	ELF1	chr5:40834740-40835790	GM12878	blood:	n/a	chr5:40835311-40835324 chr5:40835328-40835341
22	ZC3H11A	chr5:40834501-40835759	K562	blood:	n/a	n/a
23	ELF1	chr5:40834782-40835858	MCF-7	breast:	n/a	chr5:40835311-40835324 chr5:40835328-40835341
24	POLR2A	chr5:40832572-40835811	U87	brain:	n/a	n/a
25	ETS1	chr5:40834482-40835831	A549	lung:	n/a	chr5:40835326-40835342 chr5:40835368-40835379 chr5:40835363-40835380 chr5:40835366-40835380 chr5:40835369-40835380 chr5:40835329-40835338 chr5:40835327-40835338 chr5:40835370-40835383 chr5:40835327-40835337 chr5:40835363-40835380
26	POLR2A	chr5:40834771-40835873	H1-hESC	embryonic stem cell:	n/a	n/a
27	BCLAF1	chr5:40834289-40835944	GM12878	blood:	n/a	chr5:40835371-40835380 chr5:40835329-40835338
28	POLR2A	chr5:40823520-40836317	SK-N-MC	brain:	n/a	n/a
29	IRF1	chr5:40833040-40835975	K562	blood:	n/a	chr5:40835569-40835581 chr5:40834809-40834822 chr5:40835564-40835581 chr5:40835569-40835580 chr5:40834809-40834823 chr5:40835569-40835581
30	POLR2A	chr5:40829918-40836581	Hela-S3	cervix:	n/a	n/a
31	SP1	chr5:40834068-40834930	H1-hESC	embryonic stem cell:	n/a	n/a
32	MXI1	chr5:40834033-40835793	GM12878	blood:	n/a	n/a
33	POLR2A	chr5:40833859-40835989	GM12891	blood:	n/a	n/a
34	TAF1	chr5:40834774-40835959	K562	blood:	n/a	n/a
35	TAF1	chr5:40834798-40835967	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr5:40833129-40836609	GM12878	blood:	n/a	n/a
37	BRCA1	chr5:40834828-40835584	H1-hESC	embryonic stem cell:	n/a	n/a
38	ZKSCAN1	chr5:40834804-40835943	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr5:40833996-40836057	H1-hESC	embryonic stem cell:	n/a	n/a
40	PML	chr5:40833820-40836144	K562	blood:	n/a	chr5:40835321-40835329
41	RUNX3	chr5:40834744-40835765	GM12878	blood:	n/a	chr5:40834857-40834872
42	TCF7L2	chr5:40834434-40836431	Hela-S3	cervix:	n/a	n/a
43	REST	chr5:40834625-40836426	HL-60	blood:	n/a	chr5:40835379-40835392 chr5:40835696-40835709
44	WRNIP1	chr5:40833235-40836410	GM12878	blood:	n/a	n/a
45	POLR2A	chr5:40833681-40836203	HUVEC	blood vessel:	n/a	n/a
46	UBTF	chr5:40834462-40836409	K562	blood:	n/a	n/a
47	MAX	chr5:40834825-40836100	HCT-116	colon:	n/a	n/a
48	IRF1	chr5:40834129-40836010	K562	blood:	n/a	chr5:40835569-40835581 chr5:40834809-40834822 chr5:40835564-40835581 chr5:40835569-40835580 chr5:40834809-40834823 chr5:40835569-40835581
49	POLR2A	chr5:40832988-40835995	GM12892	blood:	n/a	n/a
50	POLR2A	chr5:40833376-40836533	Hela-S3	cervix:	n/a	n/a

No data

(count:42 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:40753631..40759305-chr5:40833742..40838306,12	K562	blood:
2	chr19:11491381..11491995-chr5:40834857..40835530,2	Hela-S3	cervix:
3	chr5:40762484..40765387-chr5:40833487..40838148,4	K562	blood:
4	chr15:50647406..50648205-chr5:40834671..40835432,2	Hela-S3	cervix:
5	chr15:72766307..72767210-chr5:40834451..40835447,2	Hela-S3	cervix:
6	chr5:40834401..40835296-chr5:43483773..43484582,2	Hela-S3	cervix:
7	chr5:40753823..40758906-chr5:40833676..40836936,8	MCF-7	breast:
8	chr11:73087315..73087860-chr5:40834809..40835315,2	Hela-S3	cervix:
9	chr1:16482321..16483004-chr5:40834853..40835492,2	Hela-S3	cervix:
10	chr5:40795843..40803356-chr5:40833207..40837160,32	MCF-7	breast:
11	chr18:9474867..9475442-chr5:40834265..40834948,2	Hela-S3	cervix:
12	chr5:40798384..40799086-chr5:40834783..40835322,2	MCF-7	breast:
13	chr1:145382624..145383562-chr5:40834830..40835340,2	Hela-S3	cervix:
14	chr3:130465224..130465984-chr5:40834852..40835728,2	NB4	blood:
15	chr5:40833991..40836420-chr5:41902681..41904929,3	K562	blood:
16	chr19:40336469..40336972-chr5:40834757..40835327,2	Hela-S3	cervix:
17	chr5:40833974..40834885-chr6:31508984..31509608,2	Hela-S3	cervix:
18	chr19:1103670..1104418-chr5:40834623..40835230,2	Hela-S3	cervix:
19	chr5:40834802..40835667-chr6:86388362..86388990,2	Hela-S3	cervix:
20	chr5:40752902..40758869-chr5:40832024..40838409,16	K562	blood:
21	chr5:40789707..40791650-chr5:40833757..40835320,2	K562	blood:
22	chr5:40834828..40835357-chr9:96792773..96793579,2	Hela-S3	cervix:
23	chr20:48806718..48807627-chr5:40834835..40835852,3	Hela-S3	cervix:
24	chr5:40760388..40764938-chr5:40832988..40836769,5	MCF-7	breast:
25	chr14:103988730..103989594-chr5:40834707..40835350,2	Hela-S3	cervix:
26	chr17:28804381..28804923-chr5:40834787..40835410,2	Hela-S3	cervix:
27	chr1:149858456..149859986-chr5:40833944..40836674,2	MCF-7	breast:
28	chr14:91526460..91527177-chr5:40834800..40835350,2	Hela-S3	cervix:
29	chr5:40796430..40799942-chr5:40831748..40836996,14	MCF-7	breast:
30	chr11:126138706..126139397-chr5:40834773..40835330,2	Hela-S3	cervix:
31	chr12:48448475..48449474-chr5:40834158..40834864,2	Hela-S3	cervix:
32	chr16:28834557..28835100-chr5:40834689..40835579,2	Hela-S3	cervix:
33	chr5:40797603..40798412-chr5:40834751..40835625,2	Hela-S3	cervix:
34	chr17:37617317..37618153-chr5:40834782..40835378,3	Hela-S3	cervix:
35	chr5:40790254..40794130-chr5:40832238..40836861,6	MCF-7	breast:
36	chr14:53257908..53258576-chr5:40834406..40835365,2	Hela-S3	cervix:
37	chr11:63580858..63581436-chr5:40834265..40835260,2	Hela-S3	cervix:
38	chr17:41622536..41623210-chr5:40834826..40835404,2	NB4	blood:
39	chr17:73150045..73150805-chr5:40834811..40836018,3	Hela-S3	cervix:
40	chr5:40752681..40758776-chr5:40831589..40836413,12	MCF-7	breast:
41	chr16:30006934..30007813-chr5:40834853..40835764,2	Hela-S3	cervix:
42	chr3:186524060..186524941-chr5:40834704..40835574,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
RPL37	TF binding region
SNORD72	TF binding region
ENSG00000104064	Chromatin interaction
ENSG00000158079	Chromatin interaction
ENSG00000100784	Chromatin interaction
ENSG00000168488	Chromatin interaction
ENSG00000133943	Chromatin interaction
ENSG00000151881	Chromatin interaction
ENSG00000172216	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000249492	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000054967	Chromatin interaction
ENSG00000110074	Chromatin interaction
ENSG00000149929	Chromatin interaction
ENSG00000175832	Chromatin interaction
ENSG00000113638	Chromatin interaction
ENSG00000105202	Chromatin interaction
ENSG00000166233	Chromatin interaction
ENSG00000142627	Chromatin interaction
ENSG00000240399	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000198563	Chromatin interaction
ENSG00000166165	Chromatin interaction
ENSG00000132356	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000196455	Chromatin interaction
ENSG00000017797	Chromatin interaction
ENSG00000212567	Chromatin interaction
ENSG00000163918	Chromatin interaction
ENSG00000261423	Chromatin interaction
ENSG00000169592	Chromatin interaction
ENSG00000187266	Chromatin interaction
ENSG00000182934	Chromatin interaction
ENSG00000167258	Chromatin interaction
ENSG00000167468	Chromatin interaction
ENSG00000168005	Chromatin interaction
ENSG00000205765	Chromatin interaction
ENSG00000189159	Chromatin interaction
ENSG00000203875	Chromatin interaction
ENSG00000108587	Chromatin interaction
ENSG00000100522	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10035235	0.89[JPT][hapmap]
rs10053664	0.90[JPT][hapmap];0.95[YRI][hapmap]
rs10054398	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10062565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10066459	0.84[JPT][hapmap]
rs10069737	0.84[JPT][hapmap]
rs1015027	0.84[JPT][hapmap]
rs10941525	0.84[JPT][hapmap]
rs11747210	0.89[JPT][hapmap];0.94[YRI][hapmap]
rs12517210	0.89[JPT][hapmap]
rs12520058	0.84[JPT][hapmap]
rs12523329	0.84[JPT][hapmap]
rs1363847	0.83[JPT][hapmap]
rs2270625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2291782	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3792827	0.84[JPT][hapmap]
rs3805489	0.89[JPT][hapmap]
rs3805490	0.89[JPT][hapmap]
rs3805492	0.89[JPT][hapmap]
rs3805494	0.89[JPT][hapmap]
rs3805499	0.84[JPT][hapmap]
rs4957334	0.84[JPT][hapmap]
rs6868112	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6884484	0.93[ASN][1000 genomes]
rs7719692	0.84[JPT][hapmap]
rs7721093	0.84[JPT][hapmap]
rs7725810	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
2	nsv597877	chr5:40796746-40848803	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases
3	nsv518711	chr5:40827307-40835627	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	137 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3816959	RPL37	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40831400-40835000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:40831600-40835000	Transcr. at gene 5' and 3'	K562	blood
3	chr5:40831800-40835000	Transcr. at gene 5' and 3'	A549	lung
4	chr5:40831800-40835200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
5	chr5:40832000-40835000	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
6	chr5:40832000-40835200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
7	chr5:40832200-40835000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
8	chr5:40832200-40835000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
9	chr5:40832600-40835200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
10	chr5:40832800-40835000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:40832800-40835000	Transcr. at gene 5' and 3'	NHLF	lung
12	chr5:40833000-40835000	Transcr. at gene 5' and 3'	NHEK	skin
13	chr5:40833200-40835000	Transcr. at gene 5' and 3'	Dnd41	blood
14	chr5:40833200-40835200	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
15	chr5:40833200-40835200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
16	chr5:40833200-40835400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
17	chr5:40833200-40836400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:40833400-40836000	Active TSS	Right Ventricle	heart
19	chr5:40833400-40836200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:40833600-40836000	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr5:40833600-40836200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr5:40833600-40836600	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr5:40833800-40836000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:40833800-40836000	Active TSS	Gastric	stomach
25	chr5:40833800-40836600	Active TSS	Ovary	ovary
26	chr5:40834000-40835200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
27	chr5:40834000-40836400	Active TSS	Colonic Mucosa	Colon
28	chr5:40834000-40836600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr5:40834200-40835000	Active TSS	Right Atrium	heart
30	chr5:40834200-40835200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:40834200-40835600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:40834200-40835600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:40834200-40835600	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr5:40834200-40835800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr5:40834200-40835800	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr5:40834200-40835800	Active TSS	Stomach Mucosa	stomach
37	chr5:40834200-40836000	Active TSS	Pancreas	Pancrea
38	chr5:40834200-40836000	Active TSS	Small Intestine	intestine
39	chr5:40834200-40836200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:40834200-40836200	Active TSS	Esophagus	oesophagus
41	chr5:40834200-40836200	Active TSS	Fetal Intestine Small	intestine
42	chr5:40834200-40836200	Active TSS	Left Ventricle	heart
43	chr5:40834200-40836400	Active TSS	Placenta Amnion	Placenta Amnion
44	chr5:40834200-40836600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr5:40834200-40836600	Active TSS	Brain Cingulate Gyrus	brain
46	chr5:40834400-40835000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr5:40834400-40835000	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr5:40834400-40835000	Active TSS	Primary T cells fromperipheralblood	blood
49	chr5:40834400-40835200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr5:40834400-40835600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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