Variant report

Variant	rs6735969
Chromosome Location	chr2:97548391-97548392
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	chr2:97547842..97556078-chr2:97610100..97619985,30	MCF-7	breast:
2	chr2:97548252..97550212-chr2:97588588..97591450,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168754	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs17119655	0.85[CEU][hapmap]
rs17119656	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2314651	1.00[ASN][1000 genomes]
rs4260285	0.97[ASN][1000 genomes]
rs57675226	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58984980	0.97[ASN][1000 genomes]
rs59131346	0.98[ASN][1000 genomes]
rs62152871	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62152900	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62152901	0.86[ASN][1000 genomes]
rs62152902	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62152903	0.95[ASN][1000 genomes]
rs62152904	0.94[ASN][1000 genomes]
rs62152905	0.94[ASN][1000 genomes]
rs62152906	0.94[ASN][1000 genomes]
rs62152907	0.94[ASN][1000 genomes]
rs6576990	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs6708171	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6717064	0.85[CEU][hapmap]
rs6718420	0.94[ASN][1000 genomes]
rs6721921	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs6734326	0.83[EUR][1000 genomes]
rs6734673	0.81[CEU][hapmap]
rs6746020	0.80[EUR][1000 genomes]
rs6751815	0.98[ASN][1000 genomes]
rs72811651	0.94[ASN][1000 genomes]
rs7589232	0.85[CEU][hapmap];0.90[CHB][hapmap];0.98[ASN][1000 genomes]
rs7591775	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6735969		cis	Lymphoblastoid	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97536800-97551800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr2:97536800-97555200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:97540200-97549800	Weak transcription	Liver	Liver
4	chr2:97540800-97552200	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:97542200-97553000	Weak transcription	Fetal Intestine Small	intestine
6	chr2:97542800-97557400	Enhancers	Placenta	Placenta
7	chr2:97544600-97550800	Weak transcription	Brain Angular Gyrus	brain
8	chr2:97544600-97550800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:97544600-97551800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:97544800-97549800	Weak transcription	Brain Substantia Nigra	brain
11	chr2:97544800-97550800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:97545000-97550000	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:97545400-97549600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:97545600-97550000	Enhancers	Fetal Thymus	thymus
15	chr2:97545600-97551400	Weak transcription	Fetal Brain Male	brain
16	chr2:97545800-97554200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:97546000-97555000	Enhancers	Placenta Amnion	Placenta Amnion
18	chr2:97546600-97548600	Enhancers	H9 Cell Line	embryonic stem cell
19	chr2:97546600-97549000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:97546600-97552400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr2:97546800-97548800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:97546800-97549200	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:97546800-97549400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:97546800-97551000	Enhancers	Left Ventricle	heart
25	chr2:97547000-97548400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:97547000-97548400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:97547000-97548400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
28	chr2:97547000-97548800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:97547000-97548800	Enhancers	HSMMtube	muscle
30	chr2:97547000-97549000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:97547000-97549000	Enhancers	HSMM	muscle
32	chr2:97547200-97549400	Bivalent Enhancer	Fetal Stomach	stomach
33	chr2:97547200-97549600	Weak transcription	Right Ventricle	heart
34	chr2:97547200-97550000	Weak transcription	Stomach Mucosa	stomach
35	chr2:97547200-97550400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr2:97547400-97548400	Enhancers	Duodenum Mucosa	Duodenum
37	chr2:97547400-97550800	Weak transcription	Brain Anterior Caudate	brain
38	chr2:97547400-97550800	Enhancers	Stomach Smooth Muscle	stomach
39	chr2:97547400-97553200	Weak transcription	Fetal Brain Female	brain
40	chr2:97547400-97553400	Weak transcription	GM12878-XiMat	blood
41	chr2:97547600-97548400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr2:97547600-97548400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
43	chr2:97547600-97548400	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr2:97547600-97548400	Genic enhancers	K562	blood
45	chr2:97547600-97553200	Weak transcription	Brain Germinal Matrix	brain
46	chr2:97547800-97548400	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr2:97547800-97548600	Enhancers	Spleen	Spleen
48	chr2:97547800-97549000	Weak transcription	Adipose Nuclei	Adipose
49	chr2:97547800-97549200	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr2:97547800-97550600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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