Variant report

Variant	rs6677602
Chromosome Location	chr1:227187838-227187839
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227173653..227176046-chr1:227186826..227189560,2	MCF-7	breast:
2	chr1:227176058..227178515-chr1:227186795..227190068,3	MCF-7	breast:
3	chr1:227178460..227180582-chr1:227186986..227189766,2	K562	blood:

Variant related genes	Relation type
ENSG00000233706	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1045252	0.92[CEU][hapmap]
rs1045285	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs1045286	0.92[CEU][hapmap]
rs1045287	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs1045289	0.92[CEU][hapmap]
rs1045290	0.92[CEU][hapmap]
rs11583489	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11587443	0.92[CEU][hapmap]
rs1186	0.92[CEU][hapmap]
rs12403775	0.82[CHB][hapmap]
rs12593	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1319103	0.85[CHB][hapmap]
rs1929855	0.86[CHB][hapmap]
rs1929862	0.87[CEU][hapmap]
rs2297412	0.85[CEU][hapmap]
rs2297418	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs3768419	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs3768420	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs3768425	0.92[CEU][hapmap]
rs3795445	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs3795446	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs3795449	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs3795451	0.92[CEU][hapmap];0.81[YRI][hapmap]
rs4146588	0.86[CHB][hapmap]
rs6690803	0.92[CEU][hapmap]
rs7541033	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7553837	0.92[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227163400-227191200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:227175200-227198400	Weak transcription	A549	lung
4	chr1:227175200-227210200	Weak transcription	HMEC	breast
5	chr1:227175600-227216200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:227176000-227190200	Weak transcription	Esophagus	oesophagus
7	chr1:227176000-227191800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:227176000-227216400	Weak transcription	NHLF	lung
9	chr1:227176400-227190400	Weak transcription	Osteobl	bone
10	chr1:227176600-227190000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:227177200-227188600	Weak transcription	Fetal Lung	lung
12	chr1:227177400-227255200	Weak transcription	Small Intestine	intestine
13	chr1:227178200-227188600	Weak transcription	HSMMtube	muscle
14	chr1:227178400-227190400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:227178400-227271200	Weak transcription	Psoas Muscle	Psoas
16	chr1:227178600-227206600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:227178600-227226200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:227178800-227188800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:227179000-227188400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:227179400-227188200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr1:227179400-227198400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:227179400-227204400	Weak transcription	Stomach Mucosa	stomach
23	chr1:227179400-227215000	Weak transcription	Placenta	Placenta
24	chr1:227179600-227213800	Weak transcription	NH-A	brain
25	chr1:227180800-227190200	Weak transcription	K562	blood
26	chr1:227181200-227190400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:227181600-227191200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:227181800-227188000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:227181800-227188200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:227181800-227188600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:227182000-227188200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:227182000-227190200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:227182000-227216000	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:227182200-227190200	Weak transcription	Ovary	ovary
35	chr1:227182200-227205600	Weak transcription	Fetal Brain Male	brain
36	chr1:227182400-227190800	Weak transcription	NHEK	skin
37	chr1:227182600-227188200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:227182600-227189000	Weak transcription	Fetal Brain Female	brain
39	chr1:227182600-227190000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:227182600-227190200	Weak transcription	Gastric	stomach
41	chr1:227182600-227190200	Weak transcription	Right Ventricle	heart
42	chr1:227182600-227191400	Weak transcription	Fetal Kidney	kidney
43	chr1:227182600-227206400	Weak transcription	Brain Germinal Matrix	brain
44	chr1:227182800-227188000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:227182800-227188600	Weak transcription	NHDF-Ad	bronchial
46	chr1:227182800-227224200	Weak transcription	Spleen	Spleen
47	chr1:227183000-227188200	Weak transcription	Adipose Nuclei	Adipose
48	chr1:227183000-227188200	Weak transcription	Aorta	Aorta
49	chr1:227183000-227188200	Weak transcription	Brain Anterior Caudate	brain
50	chr1:227183000-227188200	Weak transcription	Fetal Intestine Large	intestine

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