Variant report

Variant	rs35517071
Chromosome Location	chr12:31811823-31811824
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	chr12:31811819-31812713	HCT-116	colon:	n/a	n/a
2	TCF12	chr12:31811823-31812802	ECC-1	luminal epithelium:	n/a	n/a
3	IRF1	chr12:31811483-31812691	K562	blood:	n/a	chr12:31811574-31811590
4	POLR2A	chr12:31811687-31812960	SK-N-MC	brain:	n/a	n/a
5	MAX	chr12:31811391-31812902	HCT-116	colon:	n/a	n/a
6	HCFC1	chr12:31811494-31812602	K562	blood:	n/a	n/a
7	GTF2F1	chr12:31811518-31812755	Hela-S3	cervix:	n/a	n/a
8	STAT1	chr12:31811798-31812609	GM12878	blood:	n/a	n/a
9	CHD2	chr12:31811748-31812356	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F4	chr12:31811667-31812671	MCF10A-Er-Src	breast:	n/a	chr12:31812055-31812064 chr12:31812056-31812063 chr12:31812220-31812231 chr12:31812056-31812063 chr12:31812056-31812063
11	POLR2A	chr12:31811527-31812826	GM12891	blood:	n/a	n/a
12	TAF1	chr12:31811706-31812933	ECC-1	luminal epithelium:	n/a	n/a
13	SMC3	chr12:31811719-31812707	GM12878	blood:	n/a	n/a
14	HCFC1	chr12:31811693-31812989	Hela-S3	cervix:	n/a	n/a
15	FOXM1	chr12:31811800-31812714	GM12878	blood:	n/a	n/a
16	STAT3	chr12:31811726-31812995	MCF10A-Er-Src	breast:	n/a	n/a
17	MAX	chr12:31811792-31812839	HepG2	liver:	n/a	n/a
18	ZNF384	chr12:31811605-31812584	GM12878	blood:	n/a	n/a
19	MXI1	chr12:31811434-31813575	SK-N-SH	brain:	n/a	n/a
20	MAX	chr12:31811806-31813006	ECC-1	luminal epithelium:	n/a	n/a
21	TAF1	chr12:31811440-31812925	ECC-1	luminal epithelium:	n/a	n/a
22	RCOR1	chr12:31811775-31812723	K562	blood:	n/a	n/a
23	SIN3AK20	chr12:31811814-31812955	PANC-1	pancreas:	n/a	n/a
24	BRCA1	chr12:31811759-31812626	Hela-S3	cervix:	n/a	n/a
25	RCOR1	chr12:31811706-31812525	GM12878	blood:	n/a	n/a
26	TCF12	chr12:31811726-31812970	A549	lung:	n/a	n/a
27	MAX	chr12:31811766-31812912	A549	lung:	n/a	n/a
28	JUND	chr12:31811784-31812729	K562	blood:	n/a	n/a
29	MAX	chr12:31811809-31812904	SK-N-SH	brain:	n/a	n/a
30	SP1	chr12:31811664-31812911	HCT-116	colon:	n/a	chr12:31812343-31812352 chr12:31812323-31812330
31	SMC3	chr12:31811317-31812722	Hela-S3	cervix:	n/a	n/a
32	TBP	chr12:31811588-31812751	Hela-S3	cervix:	n/a	n/a
33	MAFK	chr12:31811465-31812626	Hela-S3	cervix:	n/a	n/a
34	RUNX3	chr12:31811798-31812660	GM12878	blood:	n/a	n/a
35	WRNIP1	chr12:31811509-31812820	GM12878	blood:	n/a	n/a
36	TCF12	chr12:31811788-31812992	ECC-1	luminal epithelium:	n/a	n/a
37	E2F6	chr12:31811804-31812535	A549	lung:	n/a	chr12:31812055-31812064 chr12:31812220-31812231 chr12:31812056-31812063 chr12:31812056-31812063 chr12:31812056-31812063
38	MTA3	chr12:31811409-31812839	GM12878	blood:	n/a	n/a
39	ZKSCAN1	chr12:31811569-31812782	Hela-S3	cervix:	n/a	n/a
40	MAX	chr12:31811719-31813017	A549	lung:	n/a	n/a
41	MYBL2	chr12:31811793-31812642	HepG2	liver:	n/a	n/a
42	MXI1	chr12:31811704-31812704	GM12878	blood:	n/a	n/a
43	SP1	chr12:31811731-31812866	HCT-116	colon:	n/a	chr12:31812343-31812352 chr12:31812323-31812330
44	GABPA	chr12:31811808-31812527	MCF-7	breast:	n/a	n/a
45	PML	chr12:31811775-31812745	GM12878	blood:	n/a	n/a
46	CUX1	chr12:31811797-31812612	K562	blood:	n/a	n/a
47	EP300	chr12:31811348-31812977	ECC-1	luminal epithelium:	n/a	chr12:31811367-31811381 chr12:31812079-31812093
48	TBL1XR1	chr12:31811727-31812637	GM12878	blood:	n/a	n/a
49	GATA3	chr12:31811678-31812908	A549	lung:	n/a	n/a
50	CREB1	chr12:31811820-31812678	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:31810792..31812576-chr12:31866206..31867920,2	K562	blood:
2	chr12:31476939..31478876-chr12:31810425..31813843,3	MCF-7	breast:
3	chr12:31477479..31479253-chr12:31810754..31812715,2	K562	blood:
4	chr12:31811076..31814149-chr12:31866420..31869336,3	K562	blood:
5	chr12:31810468..31812226-chr12:32831182..32833517,2	K562	blood:

Variant related genes	Relation type
METTL20	TF binding region
ENSG00000266482	Chromatin interaction
ENSG00000087470	Chromatin interaction
ENSG00000151743	Chromatin interaction
ENSG00000177340	Chromatin interaction
ENSG00000139146	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10844000	0.84[AMR][1000 genomes]
rs10844003	0.82[AMR][1000 genomes]
rs11051525	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11051541	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs11051545	0.96[AMR][1000 genomes]
rs11051555	0.82[AMR][1000 genomes]
rs12813042	0.95[AMR][1000 genomes]
rs12813399	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3850979	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7134951	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7297921	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7300260	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7302229	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7953551	0.82[AMR][1000 genomes]
rs7960893	0.95[AMR][1000 genomes]
rs7969019	0.82[AMR][1000 genomes]
rs7978407	0.93[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043010	chr12:31798446-32143151	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv541446	chr12:31798446-32143151	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3432694	chr12:31801467-32109828	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv898966	chr12:31810126-31944985	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31811200-31813200	Active TSS	Brain Hippocampus Middle	brain
2	chr12:31811200-31813200	Active TSS	Stomach Mucosa	stomach
3	chr12:31811200-31813400	Active TSS	Brain Anterior Caudate	brain
4	chr12:31811200-31813400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:31811200-31813400	Active TSS	Stomach Smooth Muscle	stomach
6	chr12:31811200-31813600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr12:31811400-31812000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:31811400-31812000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:31811400-31812000	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr12:31811400-31812000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:31811400-31812000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr12:31811400-31812000	Flanking Active TSS	Dnd41	blood
13	chr12:31811400-31812800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:31811400-31812800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr12:31811400-31813000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr12:31811400-31813000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:31811400-31813000	Active TSS	Brain Germinal Matrix	brain
18	chr12:31811400-31813000	Active TSS	Fetal Brain Male	brain
19	chr12:31811400-31813200	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr12:31811400-31813200	Active TSS	Muscle Satellite Cultured Cells	--
21	chr12:31811400-31813200	Active TSS	Brain Angular Gyrus	brain
22	chr12:31811400-31813200	Active TSS	Brain Cingulate Gyrus	brain
23	chr12:31811400-31813200	Active TSS	Brain Substantia Nigra	brain
24	chr12:31811400-31813200	Active TSS	Rectal Smooth Muscle	rectum
25	chr12:31811400-31813400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:31811400-31813400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:31811400-31813400	Active TSS	Aorta	Aorta
28	chr12:31811400-31813400	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr12:31811400-31813400	Active TSS	Left Ventricle	heart
30	chr12:31811400-31813400	Active TSS	Right Atrium	heart
31	chr12:31811400-31813600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:31811400-31813800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:31811600-31812000	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr12:31811600-31812000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr12:31811600-31812000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:31811600-31812000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr12:31811600-31812000	Flanking Active TSS	HUVEC	blood vessel
38	chr12:31811600-31812200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:31811600-31812600	Active TSS	Fetal Lung	lung
40	chr12:31811600-31812600	Active TSS	Fetal Muscle Trunk	muscle
41	chr12:31811600-31813000	Active TSS	H9 Cell Line	embryonic stem cell
42	chr12:31811600-31813000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:31811600-31813000	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr12:31811600-31813000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:31811600-31813000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:31811600-31813000	Active TSS	Lung	lung
47	chr12:31811600-31813000	Active TSS	NH-A	brain
48	chr12:31811600-31813200	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr12:31811600-31813200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:31811600-31813200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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