Variant report

Variant	rs12636956
Chromosome Location	chr3:194815783-194815784
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	NFIC	chr3:194815654-194816280	GM12878	blood:	n/a	n/a
2	EP300	chr3:194814533-194815825	ECC-1	luminal epithelium:	n/a	n/a
3	MTA3	chr3:194814804-194816186	GM12878	blood:	n/a	n/a
4	EP300	chr3:194814575-194815793	ECC-1	luminal epithelium:	n/a	n/a
5	PML	chr3:194814774-194816845	GM12878	blood:	n/a	n/a
6	ZBTB7A	chr3:194814430-194815846	ECC-1	luminal epithelium:	n/a	chr3:194815174-194815181
7	POLR2A	chr3:194815282-194816689	GM12891	blood:	n/a	n/a
8	CTCF	chr3:194815660-194815810	GM12864	blood:	n/a	n/a
9	POU2F2	chr3:194815735-194816171	GM12878	blood:	n/a	chr3:194815986-194815996 chr3:194815984-194815997 chr3:194815985-194815995 chr3:194815986-194815996 chr3:194815981-194815999 chr3:194815987-194815994 chr3:194815984-194815997 chr3:194815983-194815997 chr3:194815986-194815995
10	POLR2A	chr3:194814633-194816938	GM12892	blood:	n/a	n/a
11	POLR2A	chr3:194815330-194816554	GM12878	blood:	n/a	n/a
12	ATF2	chr3:194815626-194816200	GM12878	blood:	n/a	n/a
13	TCF12	chr3:194814468-194815853	ECC-1	luminal epithelium:	n/a	chr3:194815032-194815042 chr3:194815036-194815043 chr3:194815491-194815498 chr3:194815034-194815041
14	RELA	chr3:194814824-194816050	GM18951	blood:	n/a	n/a
15	MTA3	chr3:194814700-194816572	GM12878	blood:	n/a	n/a
16	FOXM1	chr3:194815559-194816160	GM12878	blood:	n/a	n/a
17	CEBPB	chr3:194815066-194816201	GM12878	blood:	n/a	n/a
18	RUNX3	chr3:194814695-194816771	GM12878	blood:	n/a	chr3:194816578-194816595
19	YY1	chr3:194815754-194816130	GM12891	blood:	n/a	n/a
20	NFIC	chr3:194814586-194815789	ECC-1	luminal epithelium:	n/a	n/a
21	STAT5A	chr3:194814897-194816269	GM12878	blood:	n/a	chr3:194815643-194815655
22	MYC	chr3:194815765-194816160	NB4	blood:	n/a	n/a
23	POLR2A	chr3:194815554-194816252	GM12891	blood:	n/a	n/a
24	POLR2A	chr3:194814793-194816637	GM12878	blood:	n/a	n/a
25	POU2F2	chr3:194815710-194816258	GM12878	blood:	n/a	chr3:194815986-194815996 chr3:194815984-194815997 chr3:194815985-194815995 chr3:194815986-194815996 chr3:194815981-194815999 chr3:194815987-194815994 chr3:194815984-194815997 chr3:194815983-194815997 chr3:194815986-194815995
26	POU2F2	chr3:194815703-194816309	GM12891	blood:	n/a	chr3:194815986-194815996 chr3:194815984-194815997 chr3:194815985-194815995 chr3:194815986-194815996 chr3:194815981-194815999 chr3:194815987-194815994 chr3:194815984-194815997 chr3:194815983-194815997 chr3:194815986-194815995
27	MAX	chr3:194814518-194816173	ECC-1	luminal epithelium:	n/a	chr3:194814978-194814987
28	MAX	chr3:194815769-194816049	GM12878	blood:	n/a	n/a
29	ZBTB33	chr3:194815716-194816186	GM12878	blood:	n/a	chr3:194815959-194815969
30	POLR2A	chr3:194815716-194816164	GM12891	blood:	n/a	n/a
31	RAD21	chr3:194814623-194815810	ECC-1	luminal epithelium:	n/a	n/a
32	CREB1	chr3:194815758-194816299	GM12878	blood:	n/a	n/a
33	KAP1	chr3:194815664-194816215	HEK293	kidney:	n/a	n/a
34	POLR2A	chr3:194814592-194816746	GM12892	blood:	n/a	n/a
35	POLR2A	chr3:194815235-194816299	GM12892	blood:	n/a	n/a
36	NFATC1	chr3:194815538-194816196	GM12878	blood:	n/a	n/a
37	FOXM1	chr3:194815581-194816243	GM12878	blood:	n/a	n/a
38	TEAD4	chr3:194814494-194815975	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr3:194815384-194816649	GM12891	blood:	n/a	n/a
40	POLR2A	chr3:194814682-194816516	GM12892	blood:	n/a	n/a
41	TAF1	chr3:194815755-194816128	GM12892	blood:	n/a	n/a
42	NFIC	chr3:194814552-194815852	ECC-1	luminal epithelium:	n/a	n/a
43	ZBTB33	chr3:194815674-194816144	GM12878	blood:	n/a	chr3:194815959-194815969
44	TAF1	chr3:194815731-194816172	GM12878	blood:	n/a	n/a
45	POLR2A	chr3:194815352-194816187	GM12891	blood:	n/a	n/a
46	TCF12	chr3:194814413-194815912	ECC-1	luminal epithelium:	n/a	chr3:194815032-194815042 chr3:194815036-194815043 chr3:194815491-194815498 chr3:194815034-194815041
47	POU2F2	chr3:194815694-194816293	GM12891	blood:	n/a	chr3:194815986-194815996 chr3:194815984-194815997 chr3:194815985-194815995 chr3:194815986-194815996 chr3:194815981-194815999 chr3:194815987-194815994 chr3:194815984-194815997 chr3:194815983-194815997 chr3:194815986-194815995
48	TAF1	chr3:194815752-194816164	GM12891	blood:	n/a	n/a
49	RUNX3	chr3:194814566-194816213	GM12878	blood:	n/a	n/a
50	ELF1	chr3:194814472-194816591	GM12878	blood:	n/a	chr3:194815997-194816008

Variant related genes	Relation type
XXYLT1	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12635047	0.83[ASN][1000 genomes]
rs7635512	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	esv1813153	chr3:194754532-194851746	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv878136	chr3:194779412-194845226	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194791000-194821800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:194802000-194826800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:194803200-194815800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:194804000-194818200	Weak transcription	Right Ventricle	heart
5	chr3:194806800-194826400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:194808400-194817000	Weak transcription	HepG2	liver
7	chr3:194808400-194823000	Weak transcription	Adipose Nuclei	Adipose
8	chr3:194808600-194823000	Weak transcription	K562	blood
9	chr3:194808600-194827000	Weak transcription	Fetal Brain Female	brain
10	chr3:194808800-194816400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:194808800-194816800	Weak transcription	NHEK	skin
12	chr3:194808800-194821400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:194808800-194824800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:194813400-194818000	Weak transcription	HUVEC	blood vessel
15	chr3:194814400-194816000	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr3:194814400-194816400	Enhancers	Thymus	Thymus
17	chr3:194814400-194816600	Flanking Active TSS	GM12878-XiMat	blood
18	chr3:194814400-194817000	Enhancers	Primary B cells from cord blood	blood
19	chr3:194814400-194817200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr3:194814400-194817400	Enhancers	Fetal Intestine Large	intestine
21	chr3:194814400-194817400	Enhancers	Fetal Intestine Small	intestine
22	chr3:194814400-194817400	Enhancers	Fetal Muscle Leg	muscle
23	chr3:194814400-194823000	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:194814600-194815800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:194814600-194816000	Enhancers	HSMM	muscle
26	chr3:194814600-194816200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:194814600-194816200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr3:194814600-194816400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:194814600-194816400	Enhancers	HSMMtube	muscle
30	chr3:194814600-194816600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:194814600-194816600	Enhancers	Primary hematopoietic stem cells	blood
32	chr3:194814600-194817000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:194814600-194817400	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr3:194814600-194827800	Enhancers	Fetal Heart	heart
35	chr3:194814800-194815800	Enhancers	Primary T cells from cord blood	blood
36	chr3:194814800-194815800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:194814800-194817000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:194814800-194818000	Weak transcription	Left Ventricle	heart
39	chr3:194815000-194815800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:194815000-194815800	Enhancers	Primary B cells from peripheral blood	blood
41	chr3:194815000-194816200	Enhancers	H1 Cell Line	embryonic stem cell
42	chr3:194815000-194816200	Enhancers	Placenta	Placenta
43	chr3:194815000-194816800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:194815000-194817000	Enhancers	Fetal Muscle Trunk	muscle
45	chr3:194815000-194817200	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr3:194815000-194819600	Enhancers	Fetal Thymus	thymus
47	chr3:194815200-194815800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:194815200-194816000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:194815200-194816000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:194815200-194816000	Genic enhancers	Fetal Stomach	stomach

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