Variant report

Variant	rs6540697
Chromosome Location	chr1:211807035-211807036
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:211751483..211753774-chr1:211805908..211807801,3	MCF-7	breast:
2	chr1:211805499..211810389-chr1:211816053..211819078,4	K562	blood:
3	chr1:211794683..211796296-chr1:211806280..211809015,2	MCF-7	breast:
4	chr1:211805954..211807830-chr1:211810555..211812059,2	K562	blood:

Variant related genes	Relation type
ENSG00000228792	Chromatin interaction
ENSG00000170385	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10779564	0.80[AMR][1000 genomes]
rs10779565	0.80[AMR][1000 genomes]
rs10779566	0.80[AMR][1000 genomes]
rs10863919	0.87[MEX][hapmap]
rs11119778	0.96[ASN][1000 genomes]
rs11119780	0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs11576130	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12087826	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12090722	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1530400	0.83[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs4245741	0.87[MEX][hapmap]
rs4951416	0.80[AMR][1000 genomes]
rs4951418	0.80[AMR][1000 genomes]
rs4951419	0.81[AMR][1000 genomes]
rs4951539	0.81[AMR][1000 genomes]
rs4951541	0.92[CHB][hapmap]
rs61851777	0.80[AMR][1000 genomes]
rs6540698	0.80[AMR][1000 genomes]
rs6660850	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670986	0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs6671497	0.80[AMR][1000 genomes]
rs6673372	0.87[EUR][1000 genomes]
rs6675796	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6682640	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7513348	0.81[AMR][1000 genomes]
rs7516924	0.81[EUR][1000 genomes]
rs7523748	0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs7551341	0.83[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7553718	0.83[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7554315	0.83[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs894853	0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs894855	0.80[AMR][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	nsv1010919	chr1:211804252-211823073	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6540697	C1orf107	cis	cerebellum	SCAN
rs6540697	CD34	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211800000-211807200	Enhancers	Fetal Heart	heart
2	chr1:211803400-211807600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:211803400-211807600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr1:211803600-211807200	Enhancers	Fetal Muscle Trunk	muscle
5	chr1:211803600-211807200	Enhancers	Fetal Muscle Leg	muscle
6	chr1:211803800-211807600	Enhancers	Fetal Thymus	thymus
7	chr1:211804200-211807200	Enhancers	Right Atrium	heart
8	chr1:211804200-211807200	Enhancers	Right Ventricle	heart
9	chr1:211804200-211807600	Enhancers	Left Ventricle	heart
10	chr1:211804200-211813400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:211804200-211816600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:211804400-211807400	Enhancers	Spleen	Spleen
13	chr1:211804400-211809400	Enhancers	Hela-S3	cervix
14	chr1:211805400-211807400	Enhancers	Osteobl	bone
15	chr1:211805400-211808200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:211805400-211808200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:211805600-211807200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:211805600-211807200	Enhancers	HSMM	muscle
19	chr1:211805600-211807400	Enhancers	NH-A	brain
20	chr1:211805600-211807800	Enhancers	HMEC	breast
21	chr1:211805800-211807200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:211805800-211807200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:211805800-211807200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr1:211805800-211807200	Enhancers	Rectal Smooth Muscle	rectum
25	chr1:211805800-211807200	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr1:211805800-211807200	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr1:211805800-211807200	Enhancers	NHEK	skin
28	chr1:211805800-211807400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:211805800-211807600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:211805800-211807600	Enhancers	Pancreas	Pancrea
31	chr1:211805800-211807600	Enhancers	HSMMtube	muscle
32	chr1:211805800-211808200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:211806000-211807200	Enhancers	NHLF	lung
34	chr1:211806200-211807400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:211806200-211807600	Enhancers	Liver	Liver
36	chr1:211806400-211807200	Flanking Active TSS	HepG2	liver
37	chr1:211806400-211807200	Flanking Active TSS	K562	blood
38	chr1:211806400-211807400	Enhancers	A549	lung
39	chr1:211806400-211807800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:211806600-211807200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:211806600-211807200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:211806600-211807200	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr1:211806600-211807200	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr1:211806600-211807400	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr1:211806800-211807200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:211806800-211807200	Enhancers	Fetal Stomach	stomach
47	chr1:211806800-211809200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:211806800-211809600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr1:211806800-211809600	Weak transcription	Fetal Intestine Small	intestine
50	chr1:211806800-211811600	Weak transcription	Fetal Intestine Large	intestine

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