Variant report

Variant	rs1998949
Chromosome Location	chr6:33721457-33721458
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33704352..33707039-chr6:33718768..33721610,2	MCF-7	breast:
2	chr6:33721254..33721988-chr6:33729704..33730219,2	K562	blood:
3	chr6:33711960..33715900-chr6:33717224..33721956,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161896	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10672	1.00[JPT][hapmap]
rs10947428	0.89[CEU][hapmap]
rs10947436	0.83[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs11751943	0.93[EUR][1000 genomes]
rs1318691	0.82[EUR][1000 genomes]
rs1536500	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1536501	0.89[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs1547668	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs2182658	0.82[EUR][1000 genomes]
rs2182659	0.83[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2395401	0.83[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2395446	0.82[EUR][1000 genomes]
rs2395447	0.90[EUR][1000 genomes]
rs2395448	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2967	1.00[JPT][hapmap]
rs3957165	0.83[CEU][hapmap]
rs4711350	0.83[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs4713676	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs487835	0.82[EUR][1000 genomes]
rs498114	1.00[JPT][hapmap]
rs4996878	0.91[EUR][1000 genomes]
rs4996879	0.91[EUR][1000 genomes]
rs530614	0.83[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs549652	1.00[JPT][hapmap]
rs570749	0.81[EUR][1000 genomes]
rs597386	1.00[JPT][hapmap]
rs597723	0.80[EUR][1000 genomes]
rs602399	0.83[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs608971	1.00[JPT][hapmap]
rs623813	1.00[JPT][hapmap]
rs652049	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs654682	1.00[JPT][hapmap]
rs658087	1.00[JPT][hapmap]
rs684119	1.00[JPT][hapmap]
rs688209	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs6913517	1.00[JPT][hapmap]
rs6915136	1.00[JPT][hapmap]
rs6921772	0.82[EUR][1000 genomes]
rs7449707	0.90[EUR][1000 genomes]
rs751727	0.84[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs756138	0.82[EUR][1000 genomes]
rs756139	0.82[EUR][1000 genomes]
rs764753	1.00[JPT][hapmap]
rs7739273	0.82[EUR][1000 genomes]
rs791904	0.82[EUR][1000 genomes]
rs9380379	0.83[EUR][1000 genomes]
rs943463	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs943464	0.83[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs943465	0.89[EUR][1000 genomes]
rs943472	0.83[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs943473	0.82[EUR][1000 genomes]
rs943476	0.82[EUR][1000 genomes]
rs9461905	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9461907	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9469542	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1998949	BAK1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33714800-33722600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr6:33715200-33737800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:33715600-33729400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:33717000-33723000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:33719200-33723600	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr6:33719400-33722200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:33719600-33729000	Weak transcription	Right Atrium	heart
8	chr6:33719800-33727600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:33719800-33729200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:33720200-33722400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:33720200-33722600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr6:33720200-33723000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr6:33720200-33728000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr6:33720200-33730600	Weak transcription	Spleen	Spleen
15	chr6:33720400-33723000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:33720400-33728000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:33720600-33722200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:33720600-33722400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:33720600-33722600	Weak transcription	GM12878-XiMat	blood
20	chr6:33720600-33722800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:33720600-33723000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:33720600-33729400	Weak transcription	Fetal Intestine Large	intestine
23	chr6:33720800-33726200	Weak transcription	Fetal Lung	lung
24	chr6:33721000-33722200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:33721000-33722800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:33721000-33724000	Weak transcription	Stomach Mucosa	stomach
27	chr6:33721000-33727000	Weak transcription	Fetal Intestine Small	intestine
28	chr6:33721000-33729400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr6:33721200-33728600	Weak transcription	Fetal Thymus	thymus
30	chr6:33721400-33724400	Weak transcription	Rectal Mucosa Donor 31	rectum

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