Variant report

Variant	rs3759405
Chromosome Location	chr12:51441897-51441898
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:508)
CpG islands
(count:0)
Chromatin interactive
region (count:38)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:508 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:51441512-51442395	GM12891	blood:	n/a	n/a
2	MYC	chr12:51441539-51443099	K562	blood:	n/a	n/a
3	HCFC1	chr12:51441461-51442350	K562	blood:	n/a	n/a
4	ELF1	chr12:51441465-51442435	GM12878	blood:	n/a	chr12:51441932-51441943
5	POLR2A	chr12:51441408-51442365	ECC-1	luminal epithelium:	n/a	n/a
6	TBL1XR1	chr12:51441433-51442333	K562	blood:	n/a	n/a
7	EP300	chr12:51441537-51442120	SK-N-SH_RA	brain:	n/a	n/a
8	ELF1	chr12:51441490-51442319	A549	lung:	n/a	chr12:51441932-51441943
9	SMARCC2	chr12:51441503-51442520	Hela-S3	cervix:	n/a	n/a
10	EP300	chr12:51441301-51442444	A549	lung:	n/a	n/a
11	CUX1	chr12:51441877-51442273	GM12878	blood:	n/a	n/a
12	RAD21	chr12:51441486-51441925	GM12878	blood:	n/a	chr12:51441681-51441700 chr12:51441852-51441864 chr12:51441711-51441725
13	SIX5	chr12:51441681-51442146	A549	lung:	n/a	n/a
14	TAF1	chr12:51441458-51442470	MCF-7	breast:	n/a	n/a
15	ZNF143	chr12:51441511-51442166	H1-hESC	embryonic stem cell:	n/a	chr12:51441788-51441798 chr12:51441755-51441773
16	POLR2A	chr12:51441525-51442482	ProgFib	skin:	n/a	n/a
17	POLR2A	chr12:51441567-51442204	H1-hESC	embryonic stem cell:	n/a	n/a
18	RFX5	chr12:51441479-51442757	GM12878	blood:	n/a	n/a
19	NFYB	chr12:51441772-51442387	K562	blood:	n/a	chr12:51442030-51442043 chr12:51442027-51442042
20	MYC	chr12:51441608-51442230	H1-hESC	embryonic stem cell:	n/a	n/a
21	FOXP2	chr12:51441620-51441972	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr12:51441369-51442373	SK-N-SH	brain:	n/a	n/a
23	TCF12	chr12:51441324-51442548	ECC-1	luminal epithelium:	n/a	chr12:51442366-51442374
24	SP1	chr12:51441465-51442242	GM12878	blood:	n/a	n/a
25	NR2F2	chr12:51441370-51443056	MCF-7	breast:	n/a	n/a
26	PML	chr12:51441563-51442333	GM12878	blood:	n/a	n/a
27	CHD2	chr12:51441538-51442202	HepG2	liver:	n/a	chr12:51441923-51441930
28	POLR2A	chr12:51441342-51442962	GM12892	blood:	n/a	n/a
29	CHD2	chr12:51441473-51442849	GM12878	blood:	n/a	chr12:51441923-51441930
30	SMARCB1	chr12:51441459-51442607	Hela-S3	cervix:	n/a	n/a
31	SIN3AK20	chr12:51441442-51442369	SK-N-SH	brain:	n/a	n/a
32	TBL1XR1	chr12:51441518-51442289	GM12878	blood:	n/a	n/a
33	TAF1	chr12:51441369-51442746	ECC-1	luminal epithelium:	n/a	n/a
34	BCL3	chr12:51441389-51442561	A549	lung:	n/a	n/a
35	RAD21	chr12:51441507-51441906	H1-hESC	embryonic stem cell:	n/a	chr12:51441681-51441700 chr12:51441852-51441864 chr12:51441711-51441725
36	CREB1	chr12:51441703-51442183	A549	lung:	n/a	n/a
37	ELF1	chr12:51441575-51442169	HepG2	liver:	n/a	chr12:51441932-51441943
38	NFIC	chr12:51441527-51442268	GM12878	blood:	n/a	n/a
39	POLR2A	chr12:51441434-51442741	K562	blood:	n/a	n/a
40	REST	chr12:51441364-51442406	PFSK-1	brain:	n/a	chr12:51441654-51441663
41	POLR2A	chr12:51441380-51442918	K562	blood:	n/a	n/a
42	POLR2A	chr12:51441256-51443160	SK-N-MC	brain:	n/a	n/a
43	TCF12	chr12:51441343-51442728	A549	lung:	n/a	chr12:51442366-51442374
44	MXI1	chr12:51441508-51442768	Hela-S3	cervix:	n/a	n/a
45	NFYA	chr12:51441861-51442180	GM12878	blood:	n/a	chr12:51442030-51442043 chr12:51442030-51442048
46	BCL3	chr12:51441541-51442475	A549	lung:	n/a	n/a
47	TAF1	chr12:51441532-51442330	HepG2	liver:	n/a	n/a
48	MAX	chr12:51441320-51442758	A549	lung:	n/a	n/a
49	JUND	chr12:51441563-51442099	H1-hESC	embryonic stem cell:	n/a	chr12:51442034-51442043
50	POLR2A	chr12:51441384-51443035	Hela-S3	cervix:	n/a	n/a

No data

(count:38 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51414500..51424231-chr12:51435741..51444321,19	K562	blood:
2	chr12:51441478..51442324-chr3:148847457..148848341,2	Hela-S3	cervix:
3	chr12:51441721..51442652-chr18:3449018..3449671,2	Hela-S3	cervix:
4	chr12:51440622..51443141-chr12:51753837..51755674,2	MCF-7	breast:
5	chr12:51440322..51443098-chr12:51662230..51665433,4	K562	blood:
6	chr12:51440588..51444188-chr12:51475693..51478745,10	K562	blood:
7	chr12:51440271..51447226-chr12:51475135..51479930,16	MCF-7	breast:
8	chr12:51440439..51443022-chr12:51565659..51567306,3	K562	blood:
9	chr12:31478566..31479069-chr12:51441568..51442472,2	NB4	blood:
10	chr12:51418602..51423346-chr12:51439309..51444851,15	MCF-7	breast:
11	chr12:51440619..51442939-chr12:51783521..51786364,2	MCF-7	breast:
12	chr11:18417263..18417821-chr12:51441625..51442366,2	Hela-S3	cervix:
13	chr12:51439067..51445190-chr12:51449547..51456560,11	K562	blood:
14	chr12:51440784..51442942-chr12:51664189..51666029,2	MCF-7	breast:
15	chr12:51440111..51442560-chr12:51783834..51785722,2	MCF-7	breast:
16	chr12:51441733..51442384-chr5:43313064..43313818,2	Hela-S3	cervix:
17	chr11:73587992..73588608-chr12:51441696..51442224,2	Hela-S3	cervix:
18	chr12:51429499..51431522-chr12:51440148..51442114,3	MCF-7	breast:
19	chr12:49658597..49659188-chr12:51441443..51442076,2	Hela-S3	cervix:
20	chr12:51440642..51443592-chr12:51616961..51619958,3	MCF-7	breast:
21	chr12:51156477..51159239-chr12:51440349..51444629,5	K562	blood:
22	chr12:51441202..51443113-chr12:51468336..51471322,2	K562	blood:
23	chr12:51421636..51422560-chr12:51441327..51442402,4	MCF-7	breast:
24	chr12:51440743..51444863-chr12:51448295..51453075,7	MCF-7	breast:
25	chr12:51440639..51443821-chr12:51630707..51634068,3	K562	blood:
26	chr12:51399373..51401239-chr12:51441069..51443548,3	MCF-7	breast:
27	chr12:51441021..51443304-chr12:51610017..51612719,2	MCF-7	breast:
28	chr12:51441588..51442538-chr9:98637901..98638401,2	Hela-S3	cervix:
29	chr12:51416659..51422801-chr12:51440164..51444812,17	MCF-7	breast:
30	chr12:51440554..51443122-chr12:51610984..51612842,2	K562	blood:
31	chr12:51441811..51444855-chr12:51447426..51450145,3	K562	blood:
32	chr12:51440782..51445752-chr12:51631445..51635429,5	MCF-7	breast:
33	chr12:48213487..48214096-chr12:51441793..51442565,2	Hela-S3	cervix:
34	chr12:51441619..51444815-chr12:51631402..51636504,5	K562	blood:
35	chr12:51440588..51444188-chr12:51475774..51478819,7	K562	blood:
36	chr12:51440852..51445521-chr12:51475730..51478507,6	MCF-7	breast:
37	chr12:51419291..51420223-chr12:51441428..51442247,3	MCF-7	breast:
38	chr12:51419574..51420267-chr12:51441420..51442175,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
LETMD1	TF binding region
ENSG00000163755	Chromatin interaction
ENSG00000269339	Chromatin interaction
ENSG00000139629	Chromatin interaction
ENSG00000181924	Chromatin interaction
ENSG00000050438	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000175575	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000184271	Chromatin interaction
ENSG00000175611	Chromatin interaction
ENSG00000170545	Chromatin interaction
ENSG00000134333	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000182150	Chromatin interaction
ENSG00000112972	Chromatin interaction
ENSG00000135457	Chromatin interaction
ENSG00000177426	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000139146	Chromatin interaction
ENSG00000199903	Chromatin interaction
ENSG00000183283	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10783409	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10783413	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10876127	0.91[ASN][1000 genomes]
rs10876129	0.91[ASN][1000 genomes]
rs10876130	0.85[CHB][hapmap]
rs10876131	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10876132	0.84[ASN][1000 genomes]
rs10876136	1.00[CHB][hapmap]
rs10876138	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs11169657	0.84[ASN][1000 genomes]
rs11169695	0.85[ASN][1000 genomes]
rs11169710	1.00[CHB][hapmap]
rs12379	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424509	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs12427345	0.91[ASN][1000 genomes]
rs1466579	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1486014	0.91[ASN][1000 genomes]
rs15756	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1632791	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs17125111	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2010630	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2029145	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2029146	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs224448	0.84[ASN][1000 genomes]
rs224572	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2730655	0.89[EUR][1000 genomes]
rs370462	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs427020	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs4438107	1.00[CHB][hapmap]
rs4768970	0.82[EUR][1000 genomes]
rs4991549	0.83[EUR][1000 genomes]
rs55874804	0.91[ASN][1000 genomes]
rs61934800	0.91[ASN][1000 genomes]
rs6580782	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs6580785	1.00[CHB][hapmap]
rs6580787	0.83[EUR][1000 genomes]
rs6580788	1.00[CHB][hapmap]
rs6580791	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs706805	0.84[ASN][1000 genomes]
rs7135399	0.91[ASN][1000 genomes]
rs7136960	0.91[ASN][1000 genomes]
rs7398021	0.85[AFR][1000 genomes]
rs7953867	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7971308	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976431	0.91[ASN][1000 genomes]
rs7977740	0.84[ASN][1000 genomes]
rs901313	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9739342	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3759405	KRT79	cis	cerebellum	SCAN
rs3759405	CSAD	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51440800-51442600	Active TSS	Stomach Smooth Muscle	stomach
2	chr12:51440800-51442800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:51441000-51442400	Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr12:51441000-51442400	Active TSS	Brain Angular Gyrus	brain
5	chr12:51441000-51442400	Active TSS	Osteobl	bone
6	chr12:51441000-51442600	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr12:51441000-51442600	Active TSS	NHDF-Ad	bronchial
8	chr12:51441000-51443200	Active TSS	A549	lung
9	chr12:51441000-51443400	Active TSS	GM12878-XiMat	blood
10	chr12:51441000-51443600	Active TSS	Psoas Muscle	Psoas
11	chr12:51441200-51442200	Active TSS	HepG2	liver
12	chr12:51441200-51442400	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr12:51441200-51442400	Active TSS	Brain Cingulate Gyrus	brain
14	chr12:51441200-51442400	Active TSS	Rectal Smooth Muscle	rectum
15	chr12:51441200-51442600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:51441200-51442600	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr12:51441200-51442600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:51441200-51442600	Active TSS	Primary T cells from cord blood	blood
19	chr12:51441200-51442600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:51441200-51442600	Active TSS	Brain Anterior Caudate	brain
21	chr12:51441200-51442600	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr12:51441200-51442600	Active TSS	Fetal Brain Female	brain
23	chr12:51441200-51442600	Active TSS	HSMM	muscle
24	chr12:51441200-51442800	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr12:51441200-51442800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:51441200-51442800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:51441200-51442800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:51441200-51443000	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr12:51441200-51443000	Active TSS	Fetal Kidney	kidney
30	chr12:51441200-51443000	Active TSS	Gastric	stomach
31	chr12:51441200-51443200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:51441200-51443200	Active TSS	Right Ventricle	heart
33	chr12:51441200-51443200	Active TSS	K562	blood
34	chr12:51441400-51442400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:51441400-51442400	Active TSS	Brain Hippocampus Middle	brain
36	chr12:51441400-51442400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:51441400-51442400	Active TSS	Colonic Mucosa	Colon
38	chr12:51441400-51442600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:51441400-51442600	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr12:51441400-51442600	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr12:51441400-51442600	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr12:51441400-51442600	Active TSS	Colon Smooth Muscle	Colon
43	chr12:51441400-51442600	Active TSS	Duodenum Mucosa	Duodenum
44	chr12:51441400-51442600	Active TSS	Fetal Heart	heart
45	chr12:51441400-51442600	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr12:51441400-51442600	Active TSS	Fetal Stomach	stomach
47	chr12:51441400-51442600	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr12:51441400-51442600	Active TSS	Thymus	Thymus
49	chr12:51441400-51442600	Active TSS	HSMMtube	muscle
50	chr12:51441400-51442600	Active TSS	HUVEC	blood vessel

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