Variant report

Variant	rs4251704
Chromosome Location	chr17:34135251-34135252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr17:34134341-34137752	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr17:34134902-34138247	A549	lung:	n/a	chr17:34136058-34136071 chr17:34136054-34136070 chr17:34136056-34136066 chr17:34136053-34136071 chr17:34136059-34136068
3	KAP1	chr17:34135237-34136767	U2OS	brain:	n/a	n/a
4	MAZ	chr17:34134059-34137565	IMR90	lung:	n/a	n/a
5	SREBP1	chr17:34134666-34137123	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:34134673..34137724-chr17:34141957..34146258,6	MCF-7	breast:
2	chr17:34135239..34137919-chr17:34235430..34238099,2	K562	blood:
3	chr17:34083597..34086759-chr17:34135084..34137679,3	K562	blood:
4	chr17:33913630..33915202-chr17:34134873..34137603,2	K562	blood:
5	chr17:34121885..34124383-chr17:34134953..34137697,3	MCF-7	breast:
6	chr17:33913527..33915363-chr17:34134013..34136643,3	MCF-7	breast:
7	chr17:34089535..34095936-chr17:34135210..34140609,14	MCF-7	breast:
8	chr17:33892195..33894200-chr17:34134782..34137507,2	K562	blood:

Variant related genes	Relation type
TAF15	TF binding region
ENSG00000129270	Chromatin interaction
ENSG00000266999	Chromatin interaction
ENSG00000242660	Chromatin interaction
ENSG00000006125	Chromatin interaction
ENSG00000267347	Chromatin interaction
ENSG00000266911	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10451309	0.90[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1065341	1.00[TSI][hapmap]
rs16963927	0.93[GIH][hapmap];1.00[TSI][hapmap]
rs16971600	0.93[GIH][hapmap];1.00[TSI][hapmap]
rs16971624	0.89[GIH][hapmap];1.00[TSI][hapmap]
rs2242596	0.92[JPT][hapmap]
rs2242597	1.00[JPT][hapmap]
rs2280783	0.92[JPT][hapmap]
rs2280786	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2280788	1.00[JPT][hapmap]
rs4251700	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4251710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4251739	0.83[ASN][1000 genomes]
rs4251744	0.82[EUR][1000 genomes]
rs4251776	0.93[GIH][hapmap];1.00[TSI][hapmap]
rs55792948	0.86[ASN][1000 genomes]
rs56170514	0.86[ASN][1000 genomes]
rs56262662	0.86[ASN][1000 genomes]
rs56347933	0.87[ASN][1000 genomes]
rs56382694	0.91[ASN][1000 genomes]
rs60040900	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7209512	0.82[EUR][1000 genomes]
rs8073456	0.89[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs9896368	0.85[CHD][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs9901469	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9907320	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9914929	0.85[MEX][hapmap];0.87[TSI][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4251704	RDM1	cis	lymphoblastoid	seeQTL
rs4251704	CCL5	cis	lymphoblastoid	seeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:34127000-34135400	Weak transcription	Liver	Liver
2	chr17:34127600-34135800	Weak transcription	Aorta	Aorta
3	chr17:34128800-34135400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr17:34129000-34135400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr17:34129000-34135400	Weak transcription	Spleen	Spleen
6	chr17:34129000-34135800	Weak transcription	Right Atrium	heart
7	chr17:34129200-34135400	Weak transcription	Primary T cells from cord blood	blood
8	chr17:34129200-34135400	Weak transcription	Adipose Nuclei	Adipose
9	chr17:34129200-34135400	Weak transcription	Brain Anterior Caudate	brain
10	chr17:34129200-34135400	Weak transcription	Brain Substantia Nigra	brain
11	chr17:34129200-34135600	Weak transcription	Brain Germinal Matrix	brain
12	chr17:34129200-34135600	Weak transcription	HSMMtube	muscle
13	chr17:34129200-34135800	Weak transcription	Esophagus	oesophagus
14	chr17:34129400-34135400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr17:34129400-34135400	Weak transcription	Lung	lung
16	chr17:34132000-34135400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr17:34132200-34135400	Weak transcription	Fetal Intestine Large	intestine
18	chr17:34132200-34135400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr17:34132200-34135600	Weak transcription	Fetal Heart	heart
20	chr17:34132200-34135600	Weak transcription	Placenta	Placenta
21	chr17:34132400-34135400	Weak transcription	Brain Hippocampus Middle	brain
22	chr17:34132400-34135400	Weak transcription	GM12878-XiMat	blood
23	chr17:34132400-34135600	Weak transcription	Colon Smooth Muscle	Colon
24	chr17:34132400-34135600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr17:34133200-34135600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr17:34133600-34135400	Enhancers	HUVEC	blood vessel
27	chr17:34133600-34135600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr17:34133800-34135400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr17:34133800-34135400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr17:34133800-34135400	Enhancers	HMEC	breast
31	chr17:34133800-34135400	Enhancers	K562	blood
32	chr17:34133800-34135600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr17:34134000-34135400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr17:34134000-34135400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr17:34134000-34135400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr17:34134000-34135600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr17:34134000-34135600	Enhancers	HSMM	muscle
38	chr17:34134200-34135400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr17:34134200-34135400	Enhancers	NHLF	lung
40	chr17:34134200-34135400	Enhancers	Osteobl	bone
41	chr17:34134400-34135400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr17:34134400-34135400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr17:34134400-34135400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr17:34134400-34135600	Enhancers	NHDF-Ad	bronchial
45	chr17:34134600-34135400	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr17:34134600-34135400	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr17:34134600-34135600	Enhancers	Primary hematopoietic stem cells	blood
48	chr17:34134600-34135600	Enhancers	NH-A	brain
49	chr17:34134800-34135400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr17:34134800-34135400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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