Variant report

Variant	rs227857
Chromosome Location	chr6:44704392-44704393
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:44701864..44704579-chr6:44705649..44708324,2	K562	blood:
2	chr6:44702578..44705568-chr6:44706888..44709805,2	MCF-7	breast:
3	chr6:44629725..44631733-chr6:44703945..44706239,2	MCF-7	breast:
4	chr6:44639630..44642555-chr6:44702558..44704571,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDC5L-2	chr6:44703761-44705091	XLOC_005299

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs12192367	0.89[JPT][hapmap]
rs12529522	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs12530016	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs13202672	0.83[ASN][1000 genomes]
rs13206206	0.86[ASN][1000 genomes]
rs13206526	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs1402599	0.84[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1418435	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16869119	0.88[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs16872574	0.84[ASN][1000 genomes]
rs1935549	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2139863	0.88[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs227830	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs227832	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs227833	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs227835	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs227836	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs227839	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs227840	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs227844	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs227845	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs227849	0.88[JPT][hapmap]
rs227852	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs227853	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs227854	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs2894599	0.84[ASN][1000 genomes]
rs34243039	0.81[ASN][1000 genomes]
rs34577161	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34776198	0.84[ASN][1000 genomes]
rs34817919	0.84[ASN][1000 genomes]
rs35376827	0.86[ASN][1000 genomes]
rs35856781	0.81[ASN][1000 genomes]
rs3799965	0.87[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs3799966	0.83[ASN][1000 genomes]
rs3799969	0.84[ASN][1000 genomes]
rs3799970	0.84[ASN][1000 genomes]
rs3799972	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs3799974	0.88[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs3823252	0.87[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs3997503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711797	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4714812	0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4714813	0.92[EUR][1000 genomes]
rs4714825	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4714827	0.81[ASN][1000 genomes]
rs524492	0.84[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs542444	0.87[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs562016	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs609643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs609699	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66642874	0.84[ASN][1000 genomes]
rs67597621	0.82[ASN][1000 genomes]
rs687878	0.92[EUR][1000 genomes]
rs6904015	0.82[CHB][hapmap]
rs6919161	0.94[CHB][hapmap]
rs720988	0.84[ASN][1000 genomes]
rs720989	0.81[ASN][1000 genomes]
rs72664272	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72664273	0.83[ASN][1000 genomes]
rs72664274	0.84[ASN][1000 genomes]
rs7746032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7769218	0.87[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs9463017	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9463039	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9463040	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9472331	0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9472335	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9472376	0.86[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs227857	SUPT3H	cis	multi-tissue	Pritchard

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44696000-44706000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:44701000-44704600	Enhancers	Fetal Stomach	stomach
3	chr6:44701600-44705800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:44702000-44705600	Weak transcription	Fetal Lung	lung
5	chr6:44702200-44705600	Weak transcription	Adipose Nuclei	Adipose
6	chr6:44702400-44704800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:44703200-44705400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:44703600-44705400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:44703600-44705400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:44703800-44707200	Enhancers	GM12878-XiMat	blood
11	chr6:44703800-44708400	Weak transcription	Placenta	Placenta
12	chr6:44704000-44705200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:44704000-44705400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:44704000-44705600	Weak transcription	Fetal Thymus	thymus
15	chr6:44704000-44706000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:44704000-44706200	Weak transcription	NHEK	skin
17	chr6:44704200-44705400	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:44704200-44706000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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