Variant report

Variant	rs236344
Chromosome Location	chr1:94076560-94076561
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94073816..94077242-chr1:94077483..94081240,4	MCF-7	breast:
2	chr1:94075553..94077277-chr1:94206889..94209236,2	MCF-7	breast:
3	chr1:94076543..94079128-chr1:94244196..94245876,2	MCF-7	breast:
4	chr1:94074918..94076929-chr1:94311455..94313305,2	MCF-7	breast:
5	chr1:94075678..94077839-chr1:94077927..94082069,3	K562	blood:
6	chr1:94074700..94077458-chr1:94080437..94082607,3	K562	blood:
7	chr1:94031971..94034960-chr1:94074492..94076819,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260464	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000137936	Chromatin interaction

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

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

rs_ID	r²[population]
rs11164963	0.80[MEX][hapmap]
rs12084853	0.86[MEX][hapmap]
rs12568405	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1567791	0.80[MEX][hapmap]
rs1772781	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs1772782	0.84[ASN][1000 genomes]
rs236267	0.80[ASN][1000 genomes]
rs236273	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs236277	0.80[ASN][1000 genomes]
rs236288	0.81[AMR][1000 genomes]
rs236291	0.85[AMR][1000 genomes]
rs236301	0.84[AMR][1000 genomes]
rs236306	0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.80[LWK][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs236307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs236308	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs236311	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs236312	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs236313	0.88[CHB][hapmap];0.83[CHD][hapmap];0.82[ASN][1000 genomes]
rs236343	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs236345	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs368888	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3767979	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs399649	0.88[CHB][hapmap];0.83[CHD][hapmap];0.84[ASN][1000 genomes]
rs423493	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6660740	0.86[MEX][hapmap]
rs6702036	0.80[MEX][hapmap]
rs798213	0.85[CEU][hapmap];0.88[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs798217	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs798218	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs236344	BCAR3	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94057600-94106400	Weak transcription	Primary B cells from cord blood	blood
2	chr1:94060200-94078800	Weak transcription	Colonic Mucosa	Colon
3	chr1:94061200-94078800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:94066400-94079200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:94066400-94079600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:94068200-94079200	Genic enhancers	HSMM	muscle
7	chr1:94070200-94076800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:94070800-94079200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:94071600-94079400	Weak transcription	Small Intestine	intestine
10	chr1:94071800-94078200	Enhancers	Liver	Liver
11	chr1:94071800-94079200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:94071800-94079800	Weak transcription	Fetal Kidney	kidney
13	chr1:94072200-94078400	Enhancers	Adipose Nuclei	Adipose
14	chr1:94072200-94079000	Enhancers	NHDF-Ad	bronchial
15	chr1:94072200-94079400	Weak transcription	Fetal Intestine Large	intestine
16	chr1:94072600-94078800	Enhancers	Fetal Muscle Leg	muscle
17	chr1:94072800-94078400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:94073000-94077600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr1:94073200-94077000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr1:94073600-94079200	Genic enhancers	HMEC	breast
21	chr1:94074200-94077600	Weak transcription	Fetal Brain Male	brain
22	chr1:94074200-94077600	Weak transcription	Stomach Mucosa	stomach
23	chr1:94074400-94076800	Weak transcription	Fetal Brain Female	brain
24	chr1:94074400-94077200	Weak transcription	Brain Germinal Matrix	brain
25	chr1:94074600-94078800	Weak transcription	Fetal Lung	lung
26	chr1:94074600-94079400	Weak transcription	Pancreas	Pancrea
27	chr1:94074800-94078600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:94074800-94079200	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:94075000-94079200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:94075000-94079200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:94075200-94079400	Weak transcription	Esophagus	oesophagus
32	chr1:94075400-94077800	Weak transcription	NH-A	brain
33	chr1:94075400-94078200	Weak transcription	NHLF	lung
34	chr1:94075400-94078800	Weak transcription	Ovary	ovary
35	chr1:94075400-94079200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:94075400-94079800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:94075400-94080000	Weak transcription	Fetal Thymus	thymus
38	chr1:94075600-94076800	Weak transcription	Osteobl	bone
39	chr1:94075600-94077600	Weak transcription	Right Ventricle	heart
40	chr1:94075600-94077600	Weak transcription	Spleen	Spleen
41	chr1:94075600-94077800	Weak transcription	Fetal Stomach	stomach
42	chr1:94075600-94078000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:94075600-94078200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:94075600-94078800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:94075600-94079200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:94075600-94079600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:94075600-94079800	Weak transcription	Lung	lung
48	chr1:94075600-94080600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr1:94075800-94076800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:94075800-94076800	Weak transcription	HSMMtube	muscle

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