Variant report

Variant	rs2072704
Chromosome Location	chr1:153935543-153935544
allele	C/T
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	JUND	chr1:153934980-153937002	MCF-7	breast:	n/a	chr1:153936123-153936132 chr1:153935349-153935360
2	POLR2A	chr1:153934935-153936913	HCT-116	colon:	n/a	n/a
3	POLR2A	chr1:153934997-153936778	U87	brain:	n/a	n/a
4	RUNX3	chr1:153935437-153936530	GM12878	blood:	n/a	n/a
5	FOSL2	chr1:153935086-153935677	A549	lung:	n/a	chr1:153935348-153935359
6	CHD1	chr1:153935273-153936079	GM12878	blood:	n/a	n/a
7	MYC	chr1:153935408-153936791	K562	blood:	n/a	chr1:153936027-153936037
8	BCL3	chr1:153935251-153936893	A549	lung:	n/a	chr1:153936002-153936011 chr1:153936152-153936165
9	TAF1	chr1:153935448-153937011	ECC-1	luminal epithelium:	n/a	n/a
10	STAT5A	chr1:153934887-153937016	GM12878	blood:	n/a	chr1:153936044-153936056
11	TCF7L2	chr1:153934994-153937257	Hela-S3	cervix:	n/a	n/a
12	SIN3A	chr1:153935276-153936559	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:153935309-153936901	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr1:153935528-153936509	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr1:153934960-153936931	ECC-1	luminal epithelium:	n/a	n/a
16	RCOR1	chr1:153935330-153936194	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:153935485-153936635	GM12891	blood:	n/a	n/a
18	PML	chr1:153935499-153937033	MCF-7	breast:	n/a	n/a
19	PML	chr1:153935373-153936025	K562	blood:	n/a	n/a
20	RCOR1	chr1:153935036-153937218	Hela-S3	cervix:	n/a	n/a
21	TFAP2A	chr1:153935505-153937079	Hela-S3	cervix:	n/a	chr1:153936711-153936722 chr1:153935913-153935925 chr1:153936711-153936722
22	POLR2A	chr1:153934721-153937112	Hela-S3	cervix:	n/a	n/a
23	HDAC2	chr1:153935224-153936984	MCF-7	breast:	n/a	n/a
24	POLR2A	chr1:153935414-153936837	PBDE	blood:	n/a	n/a
25	POLR2A	chr1:153935033-153936974	K562	blood:	n/a	n/a
26	TAF1	chr1:153935490-153936548	PFSK-1	brain:	n/a	n/a
27	RFX5	chr1:153935185-153937210	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr1:153935219-153936792	K562	blood:	n/a	n/a
29	MAX	chr1:153935536-153936304	K562	blood:	n/a	chr1:153936027-153936037
30	MYC	chr1:153935013-153936785	K562	blood:	n/a	chr1:153936027-153936037
31	SMARCC1	chr1:153935001-153936881	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr1:153935212-153936436	IMR90	lung:	n/a	n/a
33	POLR2A	chr1:153934983-153936911	K562	blood:	n/a	n/a
34	POLR2A	chr1:153935469-153936948	HL-60	blood:	n/a	n/a
35	STAT3	chr1:153935255-153936283	MCF10A-Er-Src	breast:	n/a	chr1:153936044-153936056
36	TCF12	chr1:153935161-153937221	A549	lung:	n/a	n/a
37	MAX	chr1:153935242-153936918	Hela-S3	cervix:	n/a	chr1:153936027-153936037
38	MAX	chr1:153934348-153937035	MCF-7	breast:	n/a	chr1:153936027-153936037
39	JUN	chr1:153934947-153937062	K562	blood:	n/a	chr1:153936123-153936132
40	PBX3	chr1:153935490-153936446	A549	lung:	n/a	chr1:153936394-153936403
41	POLR2A	chr1:153935058-153936939	HCT-116	colon:	n/a	n/a
42	POLR2A	chr1:153935531-153936819	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:153934850-153937015	MCF-7	breast:	n/a	n/a
44	RUNX3	chr1:153935141-153936878	GM12878	blood:	n/a	n/a
45	SP1	chr1:153935273-153936912	A549	lung:	n/a	chr1:153936047-153936061 chr1:153936048-153936057 chr1:153935839-153935849 chr1:153936101-153936113 chr1:153936046-153936058 chr1:153935839-153935848 chr1:153936102-153936111 chr1:153935840-153935849 chr1:153936025-153936039 chr1:153935838-153935850 chr1:153936026-153936035
46	REST	chr1:153935519-153937058	A549	lung:	n/a	chr1:153936648-153936658 chr1:153936754-153936764 chr1:153936646-153936660
47	POLR2A	chr1:153935147-153936770	U87	brain:	n/a	n/a
48	MXI1	chr1:153935076-153936910	Hela-S3	cervix:	n/a	n/a
49	NR2F2	chr1:153935081-153937016	MCF-7	breast:	n/a	n/a
50	FOSL2	chr1:153935087-153935671	SK-N-SH	brain:	n/a	chr1:153935348-153935359

No.	Distal block	Cell Line	Cell type
1	chr1:153536879..153538939-chr1:153934770..153936803,2	MCF-7	breast:
2	chr1:153935016..153935776-chr14:23564433..23565083,2	Hela-S3	cervix:
3	chr1:153935502..153936288-chr14:92505499..92506426,2	Hela-S3	cervix:
4	chr1:153935318..153936274-chr5:41870150..41870705,2	Hela-S3	cervix:
5	chr1:153935369..153936224-chr3:184079400..184079942,2	Hela-S3	cervix:
6	chr1:153935319..153935832-chr17:7387752..7388633,2	Hela-S3	cervix:
7	chr1:153598392..153603036-chr1:153933813..153937554,5	MCF-7	breast:
8	chr1:153935278..153935869-chr12:54388793..54389755,2	Hela-S3	cervix:
9	chr1:153698690..153700726-chr1:153934650..153936976,2	MCF-7	breast:
10	chr1:153742918..153749628-chr1:153933334..153942122,16	MCF-7	breast:
11	chr1:153599949..153601639-chr1:153935071..153937718,2	MCF-7	breast:
12	chr1:153935279..153936024-chr16:2301047..2301860,2	Hela-S3	cervix:
13	chr1:153604949..153608172-chr1:153935177..153937108,3	K562	blood:
14	chr1:153935357..153936246-chr14:31091282..31091843,2	Hela-S3	cervix:
15	chr1:153699434..153701690-chr1:153934593..153936387,3	MCF-7	breast:
16	chr1:153747107..153752136-chr1:153929206..153936862,9	MCF-7	breast:
17	chr1:153935466..153936188-chr16:46723180..46724080,2	Hela-S3	cervix:

Variant related genes	Relation type
CRTC2	TF binding region
ENSG00000273026	TF binding region
CREB3L4	TF binding region
ENSG00000069329	Chromatin interaction
ENSG00000083720	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000163882	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000114859	Chromatin interaction
ENSG00000100815	Chromatin interaction
ENSG00000250133	Chromatin interaction
ENSG00000167969	Chromatin interaction
ENSG00000199565	Chromatin interaction
ENSG00000248668	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000180806	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000179933	Chromatin interaction
ENSG00000092108	Chromatin interaction
ENSG00000091651	Chromatin interaction
ENSG00000100813	Chromatin interaction
ENSG00000196754	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11264522	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11264824	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs12023578	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12032520	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12033532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12039936	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12043354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12044455	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12045838	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12726350	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2297895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33998934	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34579266	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34665499	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34752019	0.85[CEU][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs35170146	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4309017	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4323749	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61804837	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61804838	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61804839	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61805526	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6427334	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6671009	0.85[CEU][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs7527406	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9427246	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' 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 miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
6	nsv872450	chr1:153889042-153937513	Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
7	nsv532552	chr1:153912047-153950752	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2072704	HAX1	cis	cerebellum	SCAN
rs2072704	SLC27A3	cis	lymphoblastoid	seeQTL
rs2072704	HAX1	cis	parietal	SCAN
rs2072704	HAX1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153931000-153935800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:153934000-153935600	Flanking Active TSS	Colonic Mucosa	Colon
3	chr1:153934000-153935800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr1:153934200-153935600	Flanking Active TSS	Fetal Brain Female	brain
5	chr1:153934200-153935800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:153934200-153935800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:153934200-153935800	Flanking Active TSS	HUVEC	blood vessel
8	chr1:153934200-153935800	Flanking Active TSS	NH-A	brain
9	chr1:153934200-153937400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:153934400-153935600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr1:153934400-153935800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:153934400-153935800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr1:153934400-153935800	Flanking Active TSS	HSMM	muscle
14	chr1:153934400-153936000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:153934400-153936000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr1:153934400-153937000	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr1:153934400-153937200	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr1:153934400-153937600	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr1:153934600-153935600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:153934600-153935600	Flanking Active TSS	Liver	Liver
21	chr1:153934600-153935600	Flanking Active TSS	Brain Anterior Caudate	brain
22	chr1:153934600-153935600	Flanking Active TSS	Brain Cingulate Gyrus	brain
23	chr1:153934600-153935600	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr1:153934600-153935600	Flanking Active TSS	Fetal Lung	lung
25	chr1:153934600-153935800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:153934600-153935800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:153934600-153935800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr1:153934600-153935800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr1:153934600-153935800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:153934600-153935800	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr1:153934600-153935800	Flanking Active TSS	Brain Angular Gyrus	brain
32	chr1:153934600-153935800	Flanking Active TSS	Placenta	Placenta
33	chr1:153934600-153935800	Flanking Active TSS	Fetal Thymus	thymus
34	chr1:153934600-153935800	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr1:153934600-153935800	Flanking Active TSS	HMEC	breast
36	chr1:153934600-153935800	Flanking Active TSS	Osteobl	bone
37	chr1:153934600-153936800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:153934600-153937000	Active TSS	Fetal Kidney	kidney
39	chr1:153934600-153937200	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr1:153934600-153937400	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr1:153934600-153937600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:153934600-153937600	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr1:153934800-153935600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr1:153934800-153935600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr1:153934800-153935600	Flanking Active TSS	Fetal Heart	heart
46	chr1:153934800-153935600	Flanking Active TSS	NHEK	skin
47	chr1:153934800-153935800	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr1:153934800-153935800	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr1:153934800-153935800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr1:153934800-153935800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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