Variant report

Variant	rs6668440
Chromosome Location	chr1:214639913-214639914
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	GATA3	chr1:214639779-214640943	T-47D	breast:	n/a	n/a
2	GATA3	chr1:214639772-214641154	MCF-7	breast:	n/a	n/a
3	GATA3	chr1:214639802-214640958	T-47D	breast:	n/a	n/a
4	TCF7L2	chr1:214639887-214640843	Hela-S3	cervix:	n/a	n/a
5	MYC	chr1:214639845-214640879	Hela-S3	cervix:	n/a	n/a
6	RFX5	chr1:214639788-214640962	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:214639824-214641104	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
PTPN14	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10494980	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10746445	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs10746446	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs10864100	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10864101	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864103	0.85[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120331	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120332	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120333	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068677	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12128034	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12739305	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739336	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12743237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12757384	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12757776	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023030	0.91[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap]
rs4130486	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs4145623	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4233301	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4233302	0.85[CHB][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4233303	0.87[ASN][1000 genomes]
rs4233304	0.85[CHB][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4233305	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4233306	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4233307	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs4269744	0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4284238	0.85[CHB][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4474219	0.85[CHB][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4480328	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4539105	0.92[CHB][hapmap]
rs4571940	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4655250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655255	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655256	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655258	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655259	0.85[CHB][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655347	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655348	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655349	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4655350	0.85[CHB][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655351	0.85[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655352	0.91[CEU][hapmap];0.80[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655355	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5020616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5020617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540830	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6540835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540836	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs6540838	0.86[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540839	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs6540841	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6661786	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6676807	0.85[CHB][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6676956	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6682847	0.84[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682987	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs6684018	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6685434	0.85[CHB][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6689084	0.85[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691633	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518513	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7525020	0.85[CHB][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7527320	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7528315	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531610	0.85[CHB][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7537274	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs7540188	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540288	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555415	0.92[CHB][hapmap];0.90[JPT][hapmap]

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214613000-214649400	Weak transcription	Lung	lung
2	chr1:214625800-214644800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:214627200-214640000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:214628600-214640600	Weak transcription	Right Atrium	heart
5	chr1:214629200-214644800	Weak transcription	Psoas Muscle	Psoas
6	chr1:214634200-214640000	Weak transcription	Fetal Kidney	kidney
7	chr1:214634400-214640000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:214634400-214644400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:214634400-214645000	Weak transcription	HUVEC	blood vessel
10	chr1:214634400-214646200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:214634800-214640000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:214635800-214645000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:214636200-214640600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:214637000-214640200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:214637200-214640000	Weak transcription	NHDF-Ad	bronchial
16	chr1:214637200-214645000	Weak transcription	Esophagus	oesophagus
17	chr1:214637400-214641400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:214637800-214640800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:214638200-214640000	Weak transcription	Fetal Intestine Large	intestine
20	chr1:214638200-214640000	Weak transcription	Pancreas	Pancrea
21	chr1:214638200-214640200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:214638200-214642200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:214638200-214644400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:214638200-214644400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:214638200-214645400	Weak transcription	Left Ventricle	heart
26	chr1:214638200-214645600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:214638200-214645800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:214638200-214647400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:214638200-214649200	Weak transcription	Aorta	Aorta
30	chr1:214638400-214640000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:214638400-214640000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:214638400-214640000	Weak transcription	Fetal Stomach	stomach
33	chr1:214638400-214640200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:214638400-214644600	Weak transcription	HSMM	muscle
35	chr1:214638400-214649000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:214638400-214649400	Weak transcription	Right Ventricle	heart
37	chr1:214638600-214640000	Weak transcription	NHLF	lung
38	chr1:214638600-214646800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:214638800-214642800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:214639200-214640000	Enhancers	NHEK	skin
41	chr1:214639400-214640400	Enhancers	Stomach Mucosa	stomach
42	chr1:214639400-214642800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:214639600-214640800	Enhancers	Placenta Amnion	Placenta Amnion
44	chr1:214639600-214641000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:214639600-214641200	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr1:214639600-214641400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:214639600-214641400	Enhancers	Colon Smooth Muscle	Colon
48	chr1:214639600-214642200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:214639800-214640000	Enhancers	Hela-S3	cervix
50	chr1:214639800-214640000	Genic enhancers	Osteobl	bone

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