Variant report

Variant	rs6677097
Chromosome Location	chr1:175123897-175123898
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:175123723..175124795-chr1:175288482..175289411,8	MCF-7	breast:
2	chr1:175123069..175124833-chr1:175288206..175289868,26	MCF-7	breast:
3	chr1:175122415..175124453-chr1:175287912..175290526,2	MCF-7	breast:
4	chr1:175123723..175124686-chr1:175286249..175287143,2	K562	blood:
5	chr1:175122852..175126073-chr1:175286636..175289998,3	MCF-7	breast:
6	chr1:175123564..175124726-chr1:175190477..175191422,8	MCF-7	breast:
7	chr1:175123599..175124675-chr1:175190411..175191492,15	MCF-7	breast:
8	chr1:175123305..175125739-chr1:175288454..175289454,12	K562	blood:

No data

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10489326	0.85[MEX][hapmap]
rs1057239	0.85[CEU][hapmap];0.85[CHB][hapmap];0.94[MEX][hapmap]
rs1057246	0.85[CEU][hapmap];0.95[MEX][hapmap]
rs1057301	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1057302	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1057305	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10912901	0.81[CEU][hapmap]
rs11580331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11583687	0.81[CEU][hapmap];0.94[MEX][hapmap]
rs11585617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094153	0.80[ASW][hapmap]
rs12747817	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1894709	0.85[CEU][hapmap];0.95[MEX][hapmap]
rs2157588	0.93[ASW][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap]
rs2285219	0.85[CEU][hapmap]
rs2685	0.85[CEU][hapmap];0.95[MEX][hapmap]
rs34370567	0.85[CEU][hapmap];0.95[MEX][hapmap]
rs34493921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650716	0.85[MEX][hapmap]
rs6425323	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659824	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681020	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683533	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6702010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929	0.92[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7512413	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521981	0.80[ASW][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	nsv522101	chr1:175109517-175151183	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv429924	chr1:175110480-175134314	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6677097	KIAA0040	cis	Lymphoblastoid	GTEx
rs6677097	KIAA0040	Cis_1M	lymphoblastoid	RTeQTL
rs6677097	KIAA0040	cis	multi-tissue	Pritchard

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175110200-175127400	Weak transcription	Left Ventricle	heart
2	chr1:175115000-175125000	Weak transcription	Right Atrium	heart
3	chr1:175120000-175139400	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:175120200-175127600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:175121400-175127600	Weak transcription	Spleen	Spleen
6	chr1:175121600-175127200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:175121600-175128400	Weak transcription	Ovary	ovary
8	chr1:175121600-175130800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:175121800-175124000	Weak transcription	Liver	Liver
10	chr1:175121800-175131200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:175122000-175128200	Weak transcription	Gastric	stomach
12	chr1:175122200-175132800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:175122200-175133400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:175122200-175136600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:175122400-175129400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:175122800-175127200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:175122800-175128200	Weak transcription	Aorta	Aorta
18	chr1:175123200-175124600	Weak transcription	Placenta	Placenta
19	chr1:175123200-175124800	Weak transcription	Right Ventricle	heart
20	chr1:175123200-175127400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:175123200-175129600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:175123600-175124000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:175123600-175125800	Enhancers	Primary B cells from peripheral blood	blood
24	chr1:175123600-175127400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr1:175123800-175124000	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr1:175123800-175124000	Bivalent Enhancer	Fetal Heart	heart
27	chr1:175123800-175124200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:175123800-175124400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:175123800-175124400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:175123800-175124400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:175123800-175124600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr1:175123800-175125000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr1:175123800-175125000	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr1:175123800-175125200	Enhancers	GM12878-XiMat	blood
35	chr1:175123800-175125600	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr1:175123800-175129400	Weak transcription	Fetal Intestine Small	intestine

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