Variant report

Variant	rs8041241
Chromosome Location	chr15:93524198-93524199
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:93517960..93519668-chr15:93524092..93526666,2	MCF-7	breast:
2	chr15:93519741..93523293-chr15:93523822..93526900,4	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10152428	1.00[CHB][hapmap]
rs10162738	1.00[ASN][1000 genomes]
rs11074124	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12900800	1.00[CHB][hapmap]
rs1406712	0.84[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1470072	0.98[EUR][1000 genomes]
rs16947284	1.00[CHB][hapmap]
rs17525576	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17610095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17610312	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17610452	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272458	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2272463	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs4778060	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs4778061	1.00[CHB][hapmap]
rs4778064	0.98[EUR][1000 genomes]
rs6497014	1.00[CHB][hapmap]
rs7166161	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs7172853	0.81[EUR][1000 genomes]
rs7173808	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174740	1.00[CHB][hapmap]
rs7180629	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8028865	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs8030239	0.88[EUR][1000 genomes]
rs8032603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
2	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking 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 miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
3	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
4	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv530847	chr15:93444024-93555676	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
6	nsv917347	chr15:93444094-93586814	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8041241	CHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93493200-93533000	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr15:93493200-93536000	Strong transcription	HSMM	muscle
3	chr15:93493200-93571000	Strong transcription	Dnd41	blood
4	chr15:93493200-93571200	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr15:93493400-93548000	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr15:93493400-93568600	Strong transcription	Liver	Liver
7	chr15:93493400-93569600	Strong transcription	Placenta	Placenta
8	chr15:93493400-93571000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:93493400-93571000	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr15:93493600-93571400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr15:93493800-93532600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:93493800-93561400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:93493800-93571400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:93494000-93568200	Strong transcription	Fetal Thymus	thymus
15	chr15:93494000-93570400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr15:93494000-93570800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:93494000-93571000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr15:93494000-93571400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:93494400-93540600	Strong transcription	Primary T cells from cord blood	blood
20	chr15:93495000-93524800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:93496600-93525800	Weak transcription	Stomach Mucosa	stomach
22	chr15:93504000-93567800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr15:93505000-93569800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr15:93506000-93569800	Strong transcription	HepG2	liver
25	chr15:93506400-93561800	Strong transcription	A549	lung
26	chr15:93506400-93569600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr15:93507000-93532800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:93508000-93532600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:93509600-93525000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:93509600-93535400	Strong transcription	Fetal Muscle Leg	muscle
31	chr15:93509600-93542400	Strong transcription	Hela-S3	cervix
32	chr15:93509600-93568000	Strong transcription	Primary B cells from cord blood	blood
33	chr15:93509600-93569600	Strong transcription	NHDF-Ad	bronchial
34	chr15:93509600-93571200	Strong transcription	Fetal Lung	lung
35	chr15:93509600-93571400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr15:93509800-93568600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr15:93509800-93572000	Strong transcription	Fetal Intestine Large	intestine
38	chr15:93512600-93529400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr15:93512800-93526200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr15:93512800-93537400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr15:93512800-93541200	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr15:93512800-93560200	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr15:93512800-93567800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr15:93512800-93567800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:93512800-93568000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr15:93513400-93545400	Strong transcription	Adipose Nuclei	Adipose
47	chr15:93513800-93560000	Strong transcription	Fetal Kidney	kidney
48	chr15:93514200-93561000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:93514200-93570800	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr15:93514400-93535400	Strong transcription	HSMMtube	muscle

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