Variant report

Variant	rs12029076
Chromosome Location	chr1:228272687-228272688
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	MXI1	chr1:228269786-228272826	IMR90	lung:	n/a	chr1:228269970-228269979
2	POLR2A	chr1:228268843-228274035	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:228272473-228273959	K562	blood:	n/a	n/a
4	POLR2A	chr1:228272687-228273955	HepG2	liver:	n/a	n/a
5	TBL1XR1	chr1:228271690-228273696	K562	blood:	n/a	n/a
6	NR2F2	chr1:228272391-228273676	K562	blood:	n/a	chr1:228272719-228272734
7	MXI1	chr1:228268732-228272801	SK-N-SH	brain:	n/a	chr1:228269970-228269979
8	POLR2A	chr1:228272328-228272703	HUVEC	blood vessel:	n/a	n/a
9	WRNIP1	chr1:228270941-228273725	GM12878	blood:	n/a	n/a
10	NFATC1	chr1:228271808-228272799	GM12878	blood:	n/a	n/a
11	CHD1	chr1:228269799-228274173	IMR90	lung:	n/a	n/a
12	POLR2A	chr1:228271444-228273196	U87	brain:	n/a	n/a
13	POLR2A	chr1:228272477-228273769	K562	blood:	n/a	n/a
14	POLR2A	chr1:228270916-228274005	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:228271548-228272794	U87	brain:	n/a	n/a
16	POLR2A	chr1:228272522-228273789	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr1:228269976-228273984	K562	blood:	n/a	n/a
18	MYC	chr1:228272658-228272773	H1-hESC	embryonic stem cell:	n/a	n/a
19	KAP1	chr1:228271584-228273557	HEK293	kidney:	n/a	n/a
20	POLR2A	chr1:228269469-228273948	IMR90	lung:	n/a	n/a
21	CTCF	chr1:228272580-228272730	HCPEpiC	choroid plexus:	n/a	chr1:228272582-228272590
22	POLR2A	chr1:228272566-228273810	K562	blood:	n/a	n/a
23	MXI1	chr1:228269824-228272838	GM12878	blood:	n/a	chr1:228269970-228269979
24	NR2F2	chr1:228271173-228273473	K562	blood:	n/a	chr1:228272389-228272404 chr1:228272719-228272734
25	POLR2A	chr1:228270000-228273944	HepG2	liver:	n/a	n/a
26	MAX	chr1:228268751-228272869	K562	blood:	n/a	chr1:228271848-228271859 chr1:228269763-228269773 chr1:228269970-228269981 chr1:228271849-228271856 chr1:228270033-228270043 chr1:228269015-228269031 chr1:228269970-228269980 chr1:228269972-228269979 chr1:228269039-228269048
27	UBTF	chr1:228272666-228272771	K562	blood:	n/a	n/a
28	POLR2A	chr1:228272686-228272698	HepG2	liver:	n/a	n/a
29	POLR2A	chr1:228269895-228273457	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:228272583-228273862	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr1:228268769-228273719	K562	blood:	n/a	n/a
32	POLR2A	chr1:228271140-228274046	A549	lung:	n/a	n/a
33	HEY1	chr1:228268975-228274841	K562	blood:	n/a	chr1:228273039-228273054 chr1:228270374-228270389 chr1:228269868-228269883
34	POLR2A	chr1:228268947-228273523	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:228272646-228273109	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228269915..228273320-chr1:228326449..228329096,4	K562	blood:
2	chr1:228272480..228275319-chr1:228642509..228645344,2	K562	blood:
3	chr1:228192379..228197446-chr1:228268248..228273367,9	MCF-7	breast:
4	chr1:228271061..228272928-chr1:228645504..228647273,2	K562	blood:
5	chr1:228271974..228275319-chr1:228643789..228645457,3	K562	blood:
6	chr1:228244560..228247525-chr1:228272017..228274884,2	MCF-7	breast:
7	chr1:228271007..228273553-chr1:228330538..228333178,2	MCF-7	breast:
8	chr1:228198470..228200225-chr1:228272240..228274901,2	K562	blood:
9	chr1:228272232..228274964-chr1:228309512..228311112,2	K562	blood:
10	chr1:228187607..228189988-chr1:228271798..228274148,2	K562	blood:
11	chr1:228272139..228273835-chr1:228675045..228676865,2	MCF-7	breast:
12	chr1:228266682..228273620-chr1:228293839..228298603,9	MCF-7	breast:
13	chr1:228267667..228275106-chr1:228326600..228331394,10	K562	blood:
14	chr1:228270694..228272754-chr8:126441550..126443960,2	MCF-7	breast:
15	chr1:228270474..228272694-chr1:228336357..228338344,2	K562	blood:
16	chr1:228131240..228133349-chr1:228272206..228274582,2	K562	blood:
17	chr1:227973508..227976414-chr1:228271906..228274660,2	K562	blood:

Variant related genes	Relation type
ARF1	TF binding region
ENSG00000154342	Chromatin interaction
ENSG00000198835	Chromatin interaction
ENSG00000143774	Chromatin interaction
ENSG00000173334	Chromatin interaction
ENSG00000168159	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000162910	Chromatin interaction
ENSG00000196890	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10916258	0.82[EUR][1000 genomes]
rs3754356	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73092904	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228271000-228272800	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr1:228271000-228273000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:228271000-228273400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:228271000-228273600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr1:228271000-228273600	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr1:228271000-228273800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr1:228271000-228274000	Flanking Active TSS	Stomach Smooth Muscle	stomach
8	chr1:228271200-228272800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
9	chr1:228271200-228273200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:228271200-228273600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:228271200-228274000	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr1:228271400-228272800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
13	chr1:228271400-228272800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr1:228271400-228272800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
15	chr1:228271400-228272800	Flanking Active TSS	Fetal Brain Female	brain
16	chr1:228271400-228273000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
17	chr1:228271400-228273000	Transcr. at gene 5' and 3'	A549	lung
18	chr1:228271400-228273200	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr1:228271400-228273400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:228271400-228273400	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr1:228271400-228273400	Flanking Active TSS	Right Ventricle	heart
22	chr1:228271400-228273600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:228271400-228273600	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr1:228271400-228273600	Transcr. at gene 5' and 3'	K562	blood
25	chr1:228271400-228273600	Transcr. at gene 5' and 3'	NHEK	skin
26	chr1:228271400-228273800	Flanking Active TSS	Left Ventricle	heart
27	chr1:228271400-228274000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr1:228271400-228274200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
29	chr1:228271600-228272800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:228271600-228272800	Flanking Active TSS	Brain Angular Gyrus	brain
31	chr1:228271600-228273200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr1:228271600-228273400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:228271600-228273600	Flanking Active TSS	Rectal Smooth Muscle	rectum
34	chr1:228271600-228273800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
35	chr1:228271600-228273800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr1:228271600-228273800	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr1:228271600-228273800	Flanking Active TSS	Colonic Mucosa	Colon
38	chr1:228271600-228274000	Flanking Active TSS	Colon Smooth Muscle	Colon
39	chr1:228271600-228274000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr1:228271600-228278600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr1:228271800-228273000	Flanking Active TSS	Brain Hippocampus Middle	brain
42	chr1:228271800-228273000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:228271800-228273000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr1:228271800-228273200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
45	chr1:228271800-228273200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:228271800-228273400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:228271800-228274000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:228271800-228274000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:228271800-228274000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr1:228272000-228272800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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