Variant report

Variant	rs10241872
Chromosome Location	chr7:120488911-120488912
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:120488217..120490012-chr7:120496005..120497661,2	MCF-7	breast:
2	chr7:120483102..120485878-chr7:120487827..120490041,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106025	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10085399	1.00[AMR][1000 genomes]
rs10085545	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs10156133	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10224694	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs10227371	1.00[AMR][1000 genomes]
rs10228463	1.00[AMR][1000 genomes]
rs10231429	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10239339	1.00[AMR][1000 genomes]
rs10243869	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10249042	0.95[AFR][1000 genomes]
rs10256185	1.00[AMR][1000 genomes]
rs10260155	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10262473	1.00[MEX][hapmap];1.00[MKK][hapmap]
rs10269373	1.00[AMR][1000 genomes]
rs10277685	1.00[AMR][1000 genomes]
rs10281679	1.00[AMR][1000 genomes]
rs12531744	1.00[AMR][1000 genomes]
rs12537910	1.00[AMR][1000 genomes]
rs12538483	1.00[AMR][1000 genomes]
rs12539312	1.00[AMR][1000 genomes]
rs12539365	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs12540028	1.00[AMR][1000 genomes]
rs12540031	1.00[AMR][1000 genomes]
rs28366865	1.00[AMR][1000 genomes]
rs28545438	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28582920	1.00[AMR][1000 genomes]
rs28627810	1.00[AMR][1000 genomes]
rs28676720	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28696320	1.00[AMR][1000 genomes]
rs6946429	1.00[AMR][1000 genomes]
rs6955429	1.00[MEX][hapmap]
rs6959281	1.00[AMR][1000 genomes]
rs6966333	1.00[AMR][1000 genomes]
rs6970044	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7791680	1.00[AMR][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	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv5929	chr7:120467591-120513472	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10241872	NCRNA00174	trans	lymphoblastoid	seeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120445200-120494400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr7:120474000-120492400	Weak transcription	Fetal Lung	lung
3	chr7:120474000-120496400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr7:120474600-120496600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr7:120476600-120492400	Weak transcription	Gastric	stomach
6	chr7:120477000-120489800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr7:120477000-120492400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr7:120477200-120496200	Weak transcription	Aorta	Aorta
9	chr7:120479600-120494000	Weak transcription	HUVEC	blood vessel
10	chr7:120482600-120495200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr7:120482600-120496200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr7:120482800-120492200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr7:120482800-120496400	Weak transcription	Liver	Liver
14	chr7:120482800-120496400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr7:120482800-120496600	Weak transcription	Stomach Mucosa	stomach
16	chr7:120483400-120496200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr7:120483400-120496400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr7:120483600-120496600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:120485000-120493800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:120485200-120496200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr7:120485200-120496200	Weak transcription	Fetal Stomach	stomach
22	chr7:120485200-120496600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr7:120485200-120496600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:120485400-120489800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:120485400-120489800	Weak transcription	Fetal Muscle Leg	muscle
26	chr7:120485400-120496400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr7:120485400-120496400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr7:120487000-120490400	Enhancers	Fetal Heart	heart
29	chr7:120487200-120490600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:120487400-120489400	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr7:120487400-120492400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr7:120487600-120489200	Enhancers	Colon Smooth Muscle	Colon
33	chr7:120487600-120495000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr7:120488200-120492400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr7:120488200-120492600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr7:120488200-120494800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr7:120488200-120496200	Weak transcription	Fetal Intestine Small	intestine
38	chr7:120488200-120496600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr7:120488200-120496600	Weak transcription	Colonic Mucosa	Colon
40	chr7:120488400-120489800	Weak transcription	Left Ventricle	heart
41	chr7:120488400-120492400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr7:120488400-120492800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr7:120488400-120496000	Weak transcription	Fetal Kidney	kidney
44	chr7:120488400-120496200	Weak transcription	Right Ventricle	heart
45	chr7:120488600-120495200	Weak transcription	Fetal Intestine Large	intestine
46	chr7:120488800-120492600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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