Variant report

Variant	rs6909895
Chromosome Location	chr6:35812092-35812093
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:41240256..41241795-chr6:35811302..35813248,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150907	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1049649	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs10947572	0.83[CEU][hapmap]
rs10947574	0.80[EUR][1000 genomes]
rs1160828	0.86[CEU][hapmap]
rs11755072	0.86[CEU][hapmap]
rs1326752	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs17653835	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs17654270	0.80[EUR][1000 genomes]
rs17705020	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2038961	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2051647	0.86[CEU][hapmap];0.85[CHB][hapmap];0.81[EUR][1000 genomes]
rs2148533	0.80[EUR][1000 genomes]
rs2301510	0.86[CEU][hapmap]
rs2395638	0.81[EUR][1000 genomes]
rs2395640	0.86[CEU][hapmap];0.85[CHB][hapmap];0.80[EUR][1000 genomes]
rs2766522	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2766527	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2766528	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2817019	0.81[EUR][1000 genomes]
rs2817027	0.82[CEU][hapmap];0.84[CHB][hapmap]
rs2859420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3213580	0.87[CEU][hapmap]
rs3761981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3891863	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs4340986	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs4713929	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59190698	0.80[EUR][1000 genomes]
rs608267	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs612262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs638600	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs639421	0.85[CEU][hapmap]
rs6457858	0.82[CEU][hapmap]
rs6457862	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs651158	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs662713	0.83[CEU][hapmap]
rs677937	0.85[CEU][hapmap]
rs6905144	0.80[EUR][1000 genomes]
rs6908433	0.86[CEU][hapmap]
rs6910906	0.81[EUR][1000 genomes]
rs6911849	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs6916941	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs6920616	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6920862	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6923015	0.85[CEU][hapmap];0.84[CHB][hapmap];0.80[EUR][1000 genomes]
rs6926156	0.80[EUR][1000 genomes]
rs6929493	0.85[CEU][hapmap]
rs6931888	0.83[CEU][hapmap]
rs6932973	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs6933241	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs721694	0.81[EUR][1000 genomes]
rs7740886	0.82[CEU][hapmap]
rs7752545	0.86[CEU][hapmap];0.85[CHB][hapmap];0.81[EUR][1000 genomes]
rs7752551	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7755022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7755600	0.86[CEU][hapmap]
rs7774060	0.81[EUR][1000 genomes]
rs879493	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs879667	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9296168	0.85[CEU][hapmap];0.84[CHB][hapmap]
rs9462128	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs9462131	0.81[EUR][1000 genomes]
rs9462132	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9462133	0.81[EUR][1000 genomes]
rs9462134	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs9462135	0.86[CEU][hapmap];0.85[CHB][hapmap];0.81[EUR][1000 genomes]
rs9462141	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs9462143	0.86[CEU][hapmap]
rs9470120	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs9470121	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs9470122	0.80[EUR][1000 genomes]
rs9470123	0.80[EUR][1000 genomes]
rs9470125	0.80[EUR][1000 genomes]
rs9470126	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9470130	0.80[EUR][1000 genomes]
rs9470131	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9470134	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9470136	0.81[EUR][1000 genomes]
rs9470138	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9470139	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9470140	0.80[EUR][1000 genomes]
rs9470141	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs9470142	0.80[EUR][1000 genomes]
rs9470144	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs9470147	0.85[CEU][hapmap];0.84[CHB][hapmap];0.80[EUR][1000 genomes]
rs9470152	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs9470153	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs9470154	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs9470155	0.85[CEU][hapmap]
rs9470156	0.85[CEU][hapmap]
rs9470162	0.85[CEU][hapmap]
rs9470171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9470172	0.85[CEU][hapmap]

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	esv3430300	chr6:35549151-35959004	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6909895	CDKN1A	cis	Esophagus Mucosa	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35787800-35855600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:35791400-35824200	Weak transcription	Fetal Brain Male	brain
3	chr6:35791600-35819800	Weak transcription	NHLF	lung
4	chr6:35798200-35823800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:35799600-35837200	Weak transcription	Fetal Kidney	kidney
6	chr6:35799800-35823000	Weak transcription	Colonic Mucosa	Colon
7	chr6:35800000-35816200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr6:35800000-35823800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:35800400-35816000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:35800400-35816200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:35800400-35816400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:35800600-35816400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:35800600-35816400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr6:35800600-35859000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:35801000-35813800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:35801000-35832600	Strong transcription	Fetal Thymus	thymus
17	chr6:35801000-35840600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:35801200-35819800	Weak transcription	Spleen	Spleen
19	chr6:35801200-35824000	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:35801200-35826400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:35801200-35837200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:35801200-35849000	Strong transcription	Dnd41	blood
23	chr6:35801400-35813600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:35801400-35816000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:35801400-35816800	Strong transcription	Primary T cells from cord blood	blood
26	chr6:35801400-35832400	Strong transcription	HepG2	liver
27	chr6:35801600-35816200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:35801600-35816200	Weak transcription	Psoas Muscle	Psoas
29	chr6:35801800-35827800	Weak transcription	Brain Substantia Nigra	brain
30	chr6:35801800-35828800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:35802000-35816200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:35802000-35824000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr6:35803000-35819800	Weak transcription	HSMMtube	muscle
34	chr6:35803000-35823600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr6:35803200-35819000	Weak transcription	Ovary	ovary
36	chr6:35803200-35823600	Weak transcription	Esophagus	oesophagus
37	chr6:35803200-35828800	Weak transcription	Pancreas	Pancrea
38	chr6:35803400-35816200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:35803400-35816400	Weak transcription	Right Ventricle	heart
40	chr6:35803400-35817000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr6:35803400-35823800	Weak transcription	Aorta	Aorta
42	chr6:35803400-35823800	Weak transcription	Small Intestine	intestine
43	chr6:35803800-35823400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr6:35804000-35823800	Weak transcription	Gastric	stomach
45	chr6:35804400-35849000	Strong transcription	K562	blood
46	chr6:35804600-35823200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr6:35805200-35816200	Weak transcription	NHDF-Ad	bronchial
48	chr6:35805400-35823800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr6:35805600-35813200	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr6:35806200-35815200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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