Variant report

Variant	rs4671583
Chromosome Location	chr2:53995680-53995681
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	POLR2A	chr2:53994390-53995707	SK-N-MC	brain:	n/a	n/a
2	HCFC1	chr2:53993642-53995965	Hela-S3	cervix:	n/a	n/a
3	NFATC1	chr2:53994351-53995784	GM12878	blood:	n/a	chr2:53994386-53994399
4	POLR2A	chr2:53994421-53995690	Raji	blood:	n/a	n/a
5	TCF12	chr2:53994390-53995785	A549	lung:	n/a	n/a
6	SIN3A	chr2:53994428-53995720	H1-hESC	embryonic stem cell:	n/a	chr2:53995165-53995178
7	TBL1XR1	chr2:53995662-53995809	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:53994388-53995728	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:53994423-53995711	GM12891	blood:	n/a	n/a
10	BCL3	chr2:53994333-53995803	A549	lung:	n/a	chr2:53994965-53994978
11	POLR2A	chr2:53994424-53996024	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr2:53994401-53997166	GM18505	blood:	n/a	n/a
13	ATF2	chr2:53994480-53995752	GM12878	blood:	n/a	n/a
14	MAX	chr2:53994396-53995781	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr2:53994009-53996575	PBDE	blood:	n/a	n/a
16	POLR2A	chr2:53994089-53995931	GM12878	blood:	n/a	n/a
17	MTA3	chr2:53994326-53995699	GM12878	blood:	n/a	n/a
18	POLR2A	chr2:53994087-53995749	K562	blood:	n/a	n/a
19	POLR2A	chr2:53994389-53995681	GM12892	blood:	n/a	n/a
20	POLR2A	chr2:53993983-53998651	GM12878	blood:	n/a	n/a
21	MAFK	chr2:53994560-53995812	Hela-S3	cervix:	n/a	chr2:53994836-53994850 chr2:53995541-53995561 chr2:53995550-53995561
22	POLR2A	chr2:53994439-53995699	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr2:53994493-53995844	H1-hESC	embryonic stem cell:	n/a	n/a
24	CHD1	chr2:53995252-53995784	H1-hESC	embryonic stem cell:	n/a	n/a
25	NRF1	chr2:53994258-53995700	SK-N-SH	brain:	n/a	chr2:53994912-53994926 chr2:53995403-53995417 chr2:53994915-53994926 chr2:53994915-53994929 chr2:53994915-53994926
26	PML	chr2:53994207-53995780	GM12878	blood:	n/a	n/a
27	POLR2A	chr2:53994075-53999332	K562	blood:	n/a	n/a
28	POLR2A	chr2:53994405-53995696	GM12892	blood:	n/a	n/a
29	POLR2A	chr2:53994377-53995761	HL-60	blood:	n/a	n/a
30	RUNX3	chr2:53994384-53995721	GM12878	blood:	n/a	n/a
31	POLR2A	chr2:53994108-53996420	Hela-S3	cervix:	n/a	n/a
32	FOXM1	chr2:53995227-53995764	GM12878	blood:	n/a	chr2:53995448-53995456
33	POLR2A	chr2:53994282-53995980	MCF10A-Er-Src	breast:	n/a	n/a
34	E2F6	chr2:53994860-53995691	H1-hESC	embryonic stem cell:	n/a	chr2:53995491-53995505 chr2:53994916-53994925 chr2:53994968-53994977
35	SIN3AK20	chr2:53994447-53995692	MCF-7	breast:	n/a	n/a
36	REST	chr2:53994375-53995721	H1-neurons	neurons:	n/a	chr2:53995392-53995410
37	MAX	chr2:53994368-53995688	A549	lung:	n/a	n/a
38	MXI1	chr2:53993988-53995837	K562	blood:	n/a	n/a
39	POLR2A	chr2:53994419-53995693	GM12892	blood:	n/a	n/a
40	MAX	chr2:53994439-53995979	NB4	blood:	n/a	chr2:53995946-53995955
41	POLR2A	chr2:53994334-53995839	GM12892	blood:	n/a	n/a
42	EP300	chr2:53994128-53995703	K562	blood:	n/a	chr2:53994922-53994938
43	MAX	chr2:53994368-53995730	A549	lung:	n/a	n/a
44	POLR2A	chr2:53994375-53995724	GM12878	blood:	n/a	n/a
45	POLR2A	chr2:53994274-53995696	GM12892	blood:	n/a	n/a
46	E2F6	chr2:53994536-53995797	A549	lung:	n/a	chr2:53995491-53995505 chr2:53994916-53994925 chr2:53994968-53994977
47	POLR2A	chr2:53993996-53995782	GM12891	blood:	n/a	n/a
48	RCOR1	chr2:53995313-53995778	K562	blood:	n/a	n/a
49	HA-E2F1	chr2:53994492-53995719	MCF-7	breast:	n/a	chr2:53995491-53995505 chr2:53994916-53994925 chr2:53994968-53994977
50	POLR2A	chr2:53994327-53995687	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:53992980..53996474-chr2:54011575..54015691,9	K562	blood:
2	chr2:53993518..53997677-chr2:54010995..54015634,7	MCF-7	breast:
3	chr2:53993579..53997009-chr2:54011416..54015067,4	MCF-7	breast:

Variant related genes	Relation type
GPR75-ASB3	TF binding region
ENSG00000068912	Chromatin interaction
ENSG00000115239	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10171954	0.87[ASN][1000 genomes]
rs10178643	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10188142	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10192626	0.94[ASN][1000 genomes]
rs10201938	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10203095	0.88[ASN][1000 genomes]
rs10490471	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs12621225	0.86[CHB][hapmap]
rs13414216	0.86[CHB][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap];0.88[ASN][1000 genomes]
rs13432632	0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2111622	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2111623	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2160929	0.82[CHB][hapmap]
rs2160931	0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2193682	0.81[JPT][hapmap]
rs2357693	0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.88[ASN][1000 genomes]
rs2542574	0.88[ASN][1000 genomes]
rs2542576	0.87[ASN][1000 genomes]
rs2542579	0.84[ASN][1000 genomes]
rs2542584	0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2542585	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.97[ASN][1000 genomes]
rs2542588	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2542593	0.92[ASN][1000 genomes]
rs2692515	0.90[ASN][1000 genomes]
rs2692518	0.91[ASN][1000 genomes]
rs2692531	0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2692532	0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2692536	0.95[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs2692537	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2909263	0.92[ASN][1000 genomes]
rs2949811	0.92[ASN][1000 genomes]
rs2949812	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.90[ASN][1000 genomes]
rs3821081	0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4413193	0.81[ASN][1000 genomes]
rs4671529	0.88[ASN][1000 genomes]
rs56173218	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6705712	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs6708095	0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs6738369	0.94[ASN][1000 genomes]
rs6743627	0.81[CHB][hapmap]
rs698854	0.86[ASN][1000 genomes]
rs7557799	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs7572776	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7573991	0.86[ASN][1000 genomes]
rs7596349	0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7601692	0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs805433	0.82[ASN][1000 genomes]
rs805436	0.84[ASN][1000 genomes]
rs805438	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs805439	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs918207	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats 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	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53994000-53995800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:53994000-53996200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:53994200-53995800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:53994200-53995800	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr2:53994200-53995800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:53994200-53995800	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr2:53994200-53995800	Active TSS	Psoas Muscle	Psoas
8	chr2:53994200-53995800	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr2:53994200-53995800	Active TSS	HMEC	breast
10	chr2:53994200-53996000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:53994200-53996000	Active TSS	GM12878-XiMat	blood
12	chr2:53994200-53996000	Active TSS	K562	blood
13	chr2:53994200-53996200	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr2:53994200-53996400	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr2:53994200-53996400	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr2:53994200-53996600	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr2:53994400-53995800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:53994400-53995800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:53994400-53995800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:53994400-53995800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:53994400-53995800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:53994400-53995800	Active TSS	Primary T cells fromperipheralblood	blood
23	chr2:53994400-53995800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:53994400-53995800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:53994400-53995800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:53994400-53995800	Active TSS	Brain Anterior Caudate	brain
27	chr2:53994400-53995800	Active TSS	Fetal Intestine Small	intestine
28	chr2:53994400-53995800	Active TSS	Fetal Kidney	kidney
29	chr2:53994400-53995800	Active TSS	Right Ventricle	heart
30	chr2:53994400-53995800	Active TSS	Dnd41	blood
31	chr2:53994400-53995800	Active TSS	NHDF-Ad	bronchial
32	chr2:53994400-53996000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr2:53994400-53996000	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr2:53994400-53996000	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr2:53994400-53996000	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr2:53994400-53996000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:53994400-53996000	Active TSS	Fetal Thymus	thymus
38	chr2:53994400-53996000	Active TSS	Hela-S3	cervix
39	chr2:53994400-53996200	Active TSS	H1 Cell Line	embryonic stem cell
40	chr2:53994400-53996200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr2:53994400-53996200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:53994400-53996200	Active TSS	Fetal Stomach	stomach
43	chr2:53994400-53996400	Active TSS	H9 Cell Line	embryonic stem cell
44	chr2:53994400-53996400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:53994600-53995800	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr2:53994600-53995800	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr2:53994600-53996000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:53994600-53996000	Active TSS	Duodenum Mucosa	Duodenum
49	chr2:53994800-53995800	Active TSS	Osteobl	bone
50	chr2:53994800-53996200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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