Variant report

Variant	rs11258500
Chromosome Location	chr10:6442854-6442855
allele	C/T
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:6319800..6323554-chr10:6441503..6444162,3	MCF-7	breast:
2	chr10:6274299..6277760-chr10:6442222..6445453,4	MCF-7	breast:
3	chr10:6240172..6247565-chr10:6441706..6450964,34	MCF-7	breast:
4	chr10:6185039..6188332-chr10:6441868..6445811,4	MCF-7	breast:
5	chr10:6130141..6132249-chr10:6442225..6444513,2	MCF-7	breast:
6	chr10:6436665..6438310-chr10:6442602..6444402,2	MCF-7	breast:
7	chr10:6264043..6266844-chr10:6441724..6444209,2	MCF-7	breast:
8	chr10:6336971..6341697-chr10:6441247..6445868,11	MCF-7	breast:
9	chr10:6335347..6345426-chr10:6438966..6446500,25	MCF-7	breast:
10	chr10:6405295..6407901-chr10:6440170..6443280,3	MCF-7	breast:
11	chr10:6355714..6359747-chr10:6439655..6444608,4	MCF-7	breast:
12	chr10:6256631..6260538-chr10:6441320..6445135,3	MCF-7	breast:
13	chr10:6241662..6248347-chr10:6438932..6450669,77	MCF-7	breast:
14	chr10:6213842..6217578-chr10:6440215..6444300,4	MCF-7	breast:
15	chr10:6242432..6246292-chr10:6442347..6445455,4	K562	blood:
16	chr10:6433781..6435958-chr10:6440894..6443926,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000213994	Chromatin interaction
ENSG00000134453	Chromatin interaction
ENSG00000226705	Chromatin interaction
ENSG00000170525	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10508308	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs10906420	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10906426	0.81[ASN][1000 genomes]
rs10906429	0.86[ASW][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11258461	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11258501	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11258515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11258589	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11596750	0.84[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs12572911	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17155850	0.85[CEU][hapmap]
rs17155855	0.85[CEU][hapmap]
rs2236380	0.84[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2296125	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2296126	0.83[CHD][hapmap]
rs35935618	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3793725	0.85[CEU][hapmap]
rs3793726	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs590467	0.85[CEU][hapmap]
rs631968	0.84[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs658648	0.92[ASN][1000 genomes]
rs681071	0.83[TSI][hapmap]
rs681604	0.92[CHB][hapmap];0.91[CHD][hapmap];0.88[TSI][hapmap];0.83[ASN][1000 genomes]
rs688853	0.85[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs71479777	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7916702	0.83[CHD][hapmap]
rs7918923	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs961203	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs9633784	0.86[AMR][1000 genomes];0.91[EUR][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	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer 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	76 gene(s)	inside rSNPs	diseases
2	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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	40 gene(s)	inside rSNPs	diseases
3	nsv430123	chr10:6309402-6448384	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv430125	chr10:6322167-6477267	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription 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	13 gene(s)	inside rSNPs	diseases
5	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11258500	RFK	trans	brain	seeQTL
rs11258500	CYP4X1	trans	brain	seeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6425600-6443600	Weak transcription	Aorta	Aorta
2	chr10:6433800-6448600	Weak transcription	Primary T cells from cord blood	blood
3	chr10:6434600-6443600	Weak transcription	Fetal Brain Female	brain
4	chr10:6436400-6443600	Weak transcription	Fetal Kidney	kidney
5	chr10:6436600-6443400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr10:6436600-6443400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr10:6437200-6444000	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr10:6437600-6444400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr10:6439200-6443400	Weak transcription	NHEK	skin
10	chr10:6440400-6443400	Enhancers	Brain Substantia Nigra	brain
11	chr10:6440400-6443600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr10:6440600-6443600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr10:6440600-6444000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr10:6440800-6443600	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr10:6440800-6443600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr10:6441000-6443800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr10:6441200-6443400	Weak transcription	Adipose Nuclei	Adipose
18	chr10:6441200-6443400	Enhancers	Brain Anterior Caudate	brain
19	chr10:6441200-6443600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr10:6441200-6443600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr10:6441200-6443600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr10:6441400-6443400	Enhancers	Primary hematopoietic stem cells	blood
23	chr10:6441400-6443600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr10:6441400-6443600	Weak transcription	Colon Smooth Muscle	Colon
25	chr10:6441400-6444000	Enhancers	Primary B cells from peripheral blood	blood
26	chr10:6441600-6443400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr10:6441600-6443400	Weak transcription	HMEC	breast
28	chr10:6441600-6443600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr10:6441600-6443600	Enhancers	Liver	Liver
30	chr10:6441800-6443000	Weak transcription	NHLF	lung
31	chr10:6441800-6443200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr10:6441800-6443200	Weak transcription	HUVEC	blood vessel
33	chr10:6441800-6445000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr10:6442000-6443200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr10:6442000-6443200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr10:6442000-6443200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr10:6442000-6443400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr10:6442000-6443400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr10:6442000-6443400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr10:6442000-6443600	Weak transcription	Dnd41	blood
41	chr10:6442000-6447200	Weak transcription	Spleen	Spleen
42	chr10:6442200-6443000	Enhancers	Brain Cingulate Gyrus	brain
43	chr10:6442200-6443200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr10:6442200-6443200	Weak transcription	Placenta	Placenta
45	chr10:6442200-6443200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr10:6442200-6443200	Weak transcription	NH-A	brain
47	chr10:6442200-6443400	Weak transcription	Colonic Mucosa	Colon
48	chr10:6442200-6443400	Weak transcription	Fetal Stomach	stomach
49	chr10:6442200-6443400	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr10:6442200-6443600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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