Variant report

Variant	rs6902440
Chromosome Location	chr6:134287736-134287737
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:133134456..133137202-chr6:134285712..134288526,2	MCF-7	breast:
2	chr6:134258577..134261545-chr6:134287191..134289671,3	K562	blood:
3	chr6:134280961..134282692-chr6:134285960..134288759,2	MCF-7	breast:
4	chr6:134286415..134288392-chr6:134289400..134290957,2	K562	blood:
5	chr6:134286093..134287998-chr6:134291720..134294657,2	K562	blood:

Variant related genes	Relation type
ENSG00000206754	Chromatin interaction
ENSG00000112306	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10485159	1.00[JPT][hapmap]
rs17063199	1.00[JPT][hapmap]
rs17063210	1.00[JPT][hapmap]
rs17063219	1.00[JPT][hapmap]
rs2220134	0.90[YRI][hapmap]
rs2239558	0.92[EUR][1000 genomes]
rs2268068	1.00[JPT][hapmap]
rs2273097	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34569027	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777896	1.00[CHB][hapmap];0.96[EUR][1000 genomes]
rs3777899	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3822940	1.00[JPT][hapmap]
rs41286224	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4896015	1.00[JPT][hapmap]
rs4896017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56011629	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57486657	0.95[EUR][1000 genomes]
rs60898069	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6938805	1.00[JPT][hapmap]
rs73548792	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73774169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73774170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9483631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9483632	1.00[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs9483634	1.00[CHB][hapmap];0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9483635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9483639	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs9493768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493770	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs9493771	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493773	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9493774	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9493777	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9493778	0.90[YRI][hapmap]
rs9493780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9493783	0.90[YRI][hapmap]
rs9493786	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34122	chr6:134089019-134378252	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6902440	TBPL1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:134275400-134289200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:134276200-134299000	Weak transcription	Fetal Intestine Small	intestine
3	chr6:134276200-134303000	Weak transcription	HSMMtube	muscle
4	chr6:134276400-134290800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:134276400-134291000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:134276600-134288600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:134276600-134288800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:134276600-134288800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:134276600-134288800	Weak transcription	HSMM	muscle
10	chr6:134276600-134293000	Weak transcription	Fetal Lung	lung
11	chr6:134276600-134302800	Weak transcription	Fetal Kidney	kidney
12	chr6:134276600-134314000	Weak transcription	Thymus	Thymus
13	chr6:134277400-134288000	Weak transcription	NHLF	lung
14	chr6:134278000-134303600	Weak transcription	Dnd41	blood
15	chr6:134279400-134298800	Weak transcription	Psoas Muscle	Psoas
16	chr6:134279800-134294200	Weak transcription	Primary T cells from cord blood	blood
17	chr6:134280400-134304200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:134280600-134293000	Weak transcription	Liver	Liver
19	chr6:134280600-134312200	Weak transcription	Lung	lung
20	chr6:134281000-134294400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:134281400-134288800	Weak transcription	A549	lung
22	chr6:134281400-134289800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:134281400-134298800	Weak transcription	Ovary	ovary
24	chr6:134282000-134288200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:134282000-134298800	Weak transcription	Gastric	stomach
26	chr6:134282400-134289200	Genic enhancers	K562	blood
27	chr6:134282600-134302000	Weak transcription	Placenta	Placenta
28	chr6:134283000-134291000	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr6:134283000-134294200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr6:134283200-134289800	Weak transcription	Right Atrium	heart
31	chr6:134283200-134305600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:134283400-134288800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:134283400-134289800	Weak transcription	Spleen	Spleen
34	chr6:134283400-134290800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:134283400-134293600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:134283600-134288600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:134283600-134290400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr6:134283600-134290800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:134283600-134290800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr6:134283600-134290800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr6:134283800-134288200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:134284000-134288600	Weak transcription	NHEK	skin
43	chr6:134284000-134290800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:134284200-134288200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:134285000-134316600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:134285600-134288600	Weak transcription	Osteobl	bone
47	chr6:134285800-134288800	Enhancers	Primary B cells from cord blood	blood
48	chr6:134285800-134288800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr6:134285800-134289000	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr6:134285800-134289000	Enhancers	Primary T killer memory cells from peripheral blood	blood

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