Variant report

Variant	rs7234029
Chromosome Location	chr18:12877060-12877061
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	chr18:12875735..12879004-chr18:12882434..12885829,5	MCF-7	breast:
2	chr18:12875420..12877466-chr18:12879544..12881307,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175354	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11875687	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16939895	0.85[CEU][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2847297	0.90[JPT][hapmap]
rs34846641	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs482160	0.87[EUR][1000 genomes]
rs484020	0.85[CEU][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs487273	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs514000	0.88[EUR][1000 genomes]
rs515151	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs534911	0.87[EUR][1000 genomes]
rs547268	0.85[CEU][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs579052	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs612058	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs637643	1.00[YRI][hapmap]
rs6505765	0.85[JPT][hapmap]
rs657555	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs658158	0.89[EUR][1000 genomes]
rs7241016	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8083786	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8084365	0.98[AFR][1000 genomes]
rs8091305	0.83[ASW][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs8091566	0.87[EUR][1000 genomes]
rs8098730	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs9959061	1.00[ASW][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs9959425	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9961931	0.83[AFR][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	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
4	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
6	nsv909407	chr18:12877060-12917703	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7234029	CDH24	trans	parietal	SCAN
rs7234029	MC5R	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12838800-12879000	Weak transcription	Psoas Muscle	Psoas
2	chr18:12844200-12879800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr18:12857800-12881600	Weak transcription	Fetal Stomach	stomach
4	chr18:12863000-12879000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr18:12863000-12879200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr18:12863200-12879000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr18:12863200-12879800	Weak transcription	Hela-S3	cervix
8	chr18:12863200-12880200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr18:12863400-12879200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr18:12863400-12879800	Weak transcription	NHEK	skin
11	chr18:12863400-12881400	Weak transcription	Right Atrium	heart
12	chr18:12863600-12880000	Weak transcription	Esophagus	oesophagus
13	chr18:12863600-12882000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr18:12863800-12878600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr18:12863800-12880000	Weak transcription	Small Intestine	intestine
16	chr18:12863800-12880200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr18:12864400-12880000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr18:12864800-12878600	Weak transcription	Lung	lung
19	chr18:12865000-12881800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr18:12865200-12879800	Weak transcription	Fetal Lung	lung
21	chr18:12865800-12879200	Weak transcription	Pancreas	Pancrea
22	chr18:12865800-12883000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr18:12868200-12877400	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr18:12868400-12877200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr18:12868600-12879000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr18:12869000-12879400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr18:12872400-12881600	Weak transcription	Ovary	ovary
28	chr18:12873400-12879800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr18:12874200-12879600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr18:12874400-12880200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr18:12874600-12879200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr18:12875200-12877800	Enhancers	K562	blood
33	chr18:12875600-12877200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
34	chr18:12875600-12882800	Enhancers	Primary B cells from peripheral blood	blood
35	chr18:12875800-12877600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr18:12875800-12879000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr18:12875800-12879800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr18:12875800-12879800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr18:12875800-12879800	Weak transcription	Brain Angular Gyrus	brain
40	chr18:12875800-12882000	Weak transcription	HSMM	muscle
41	chr18:12876000-12878000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr18:12876000-12878800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr18:12876000-12879000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr18:12876000-12879200	Weak transcription	Liver	Liver
45	chr18:12876000-12879600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr18:12876000-12882000	Weak transcription	Fetal Intestine Large	intestine
47	chr18:12876200-12877400	Weak transcription	Spleen	Spleen
48	chr18:12876200-12877800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr18:12876200-12878600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr18:12876200-12878800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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