Variant report

Variant	rs6677965
Chromosome Location	chr1:165811729-165811730
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:165740929..165742597-chr1:165810397..165813179,2	K562	blood:
2	chr1:165734875..165737199-chr1:165810836..165813345,2	K562	blood:
3	chr1:165654373..165656083-chr1:165811609..165814179,2	K562	blood:
4	chr1:165806807..165812397-chr1:165814507..165819170,6	MCF-7	breast:
5	chr1:165810645..165813480-chr1:165823292..165825548,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10737519	0.96[ASN][1000 genomes]
rs10753694	0.93[ASN][1000 genomes]
rs10800162	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs10918291	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10918294	0.88[ASN][1000 genomes]
rs11590711	0.95[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[ASN][1000 genomes]
rs12041574	0.87[CHB][hapmap]
rs1934275	0.93[ASN][1000 genomes]
rs2185268	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.99[ASN][1000 genomes]
rs34800847	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4483381	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4535982	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4548416	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657481	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[YRI][hapmap];0.91[ASN][1000 genomes]
rs6426941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6678380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682894	0.94[ASN][1000 genomes]
rs6684773	1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs6686237	0.88[ASN][1000 genomes]
rs6690966	0.93[ASN][1000 genomes]
rs6702462	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7517175	1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs7539793	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv517792	chr1:165785503-165811729	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
3	esv2830094	chr1:165785503-165840411	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
4	nsv818544	chr1:165797966-165811729	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
5	nsv548097	chr1:165797966-165825166	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6677965	TOMM40L	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165798800-165811800	Weak transcription	Primary B cells from cord blood	blood
2	chr1:165798800-165814200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr1:165799000-165811800	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:165799000-165811800	Weak transcription	Fetal Intestine Large	intestine
5	chr1:165799000-165811800	Weak transcription	Fetal Stomach	stomach
6	chr1:165799000-165818200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:165799200-165815800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:165806400-165811800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:165807600-165812800	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr1:165808200-165814200	Enhancers	Duodenum Mucosa	Duodenum
11	chr1:165809600-165812600	Enhancers	Fetal Heart	heart
12	chr1:165809600-165812600	Enhancers	Fetal Intestine Small	intestine
13	chr1:165810600-165811800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:165810600-165812000	Enhancers	A549	lung
15	chr1:165810600-165812400	Enhancers	H1 Cell Line	embryonic stem cell
16	chr1:165810600-165812400	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr1:165810600-165812400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr1:165810600-165812400	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr1:165810600-165812400	Flanking Active TSS	Dnd41	blood
20	chr1:165810600-165812400	Enhancers	HepG2	liver
21	chr1:165810600-165812600	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr1:165810600-165812800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr1:165810600-165812800	Enhancers	HMEC	breast
24	chr1:165810600-165813000	Enhancers	Pancreas	Pancrea
25	chr1:165810600-165813200	Enhancers	Psoas Muscle	Psoas
26	chr1:165810600-165813400	Enhancers	Stomach Mucosa	stomach
27	chr1:165810800-165811800	Enhancers	HSMM	muscle
28	chr1:165810800-165811800	Enhancers	Osteobl	bone
29	chr1:165810800-165812000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:165810800-165812000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:165810800-165812000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:165810800-165812000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:165810800-165812000	Enhancers	NH-A	brain
34	chr1:165810800-165812000	Enhancers	NHLF	lung
35	chr1:165810800-165812200	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr1:165810800-165812200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:165810800-165812400	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr1:165810800-165812400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:165810800-165812400	Enhancers	H9 Cell Line	embryonic stem cell
40	chr1:165810800-165812400	Enhancers	Right Atrium	heart
41	chr1:165810800-165812400	Enhancers	Right Ventricle	heart
42	chr1:165810800-165812400	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr1:165810800-165812800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:165810800-165812800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:165810800-165812800	Enhancers	NHEK	skin
46	chr1:165810800-165813000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:165810800-165813000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:165810800-165813000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:165810800-165813000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:165810800-165813000	Enhancers	Gastric	stomach

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