Variant report

Variant	rs7258909
Chromosome Location	chr19:36377999-36378000
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36377925..36382197-chr19:36388677..36391097,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167604	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs11084834	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11878547	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11880909	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11881358	1.00[EUR][1000 genomes]
rs11881364	1.00[EUR][1000 genomes]
rs11881451	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16960862	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16970735	1.00[EUR][1000 genomes]
rs16970737	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16970742	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16970744	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17173033	0.85[ASN][1000 genomes]
rs172985	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1802029	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2227909	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs230260	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs230261	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs230262	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs230263	1.00[EUR][1000 genomes]
rs230264	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs230265	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs230266	1.00[EUR][1000 genomes]
rs230267	1.00[EUR][1000 genomes]
rs230268	0.91[EUR][1000 genomes]
rs230269	1.00[EUR][1000 genomes]
rs2871778	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs33964243	0.90[ASN][1000 genomes]
rs34006827	1.00[EUR][1000 genomes]
rs35423326	1.00[EUR][1000 genomes]
rs376240	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs392702	0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs393116	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs401824	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs404299	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs412175	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs417786	0.86[EUR][1000 genomes]
rs437168	1.00[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs443186	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs447783	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55797913	1.00[EUR][1000 genomes]
rs55816190	1.00[EUR][1000 genomes]
rs56264349	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57053076	1.00[EUR][1000 genomes]
rs57668132	1.00[EUR][1000 genomes]
rs58098901	1.00[EUR][1000 genomes]
rs58109577	1.00[EUR][1000 genomes]
rs58291714	0.95[EUR][1000 genomes]
rs58422001	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs58504183	0.81[EUR][1000 genomes]
rs58551711	0.81[EUR][1000 genomes]
rs59123406	1.00[EUR][1000 genomes]
rs59658571	1.00[EUR][1000 genomes]
rs60268250	0.95[EUR][1000 genomes]
rs60576074	0.95[EUR][1000 genomes]
rs60869994	0.95[EUR][1000 genomes]
rs60935148	0.81[EUR][1000 genomes]
rs61623584	1.00[EUR][1000 genomes]
rs619833	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7251744	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251879	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7252902	0.88[ASN][1000 genomes]
rs7253040	0.90[ASN][1000 genomes]
rs7253086	0.81[EUR][1000 genomes]
rs7253826	0.90[ASN][1000 genomes]
rs7254113	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7256433	0.81[EUR][1000 genomes]
rs7257789	0.82[ASW][hapmap];0.83[YRI][hapmap]
rs7258154	0.90[ASN][1000 genomes]
rs7258214	0.97[ASN][1000 genomes]
rs73590883	0.85[EUR][1000 genomes]
rs73594463	0.81[EUR][1000 genomes]
rs73599600	0.81[EUR][1000 genomes]
rs73928331	0.90[EUR][1000 genomes]
rs73928332	1.00[EUR][1000 genomes]
rs73928333	1.00[EUR][1000 genomes]
rs807660	1.00[EUR][1000 genomes]
rs8105153	0.83[CHD][hapmap];0.90[ASN][1000 genomes]
rs8106480	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8106495	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8106732	1.00[EUR][1000 genomes]
rs8108360	0.90[ASN][1000 genomes]
rs8108459	0.90[ASN][1000 genomes]
rs8110231	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8110926	1.00[EUR][1000 genomes]
rs8111209	1.00[EUR][1000 genomes]
rs8111348	1.00[EUR][1000 genomes]
rs8111740	0.90[ASN][1000 genomes]
rs8113524	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8113704	1.00[ASW][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs879407	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9749325	1.00[EUR][1000 genomes]
rs9749492	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
5	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv833812	chr19:36331913-36507594	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv833813	chr19:36341181-36499431	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	esv3373737	chr19:36376137-36378685	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7258909	LRFN3	cis	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36360200-36379000	Weak transcription	Aorta	Aorta
2	chr19:36361000-36389000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:36361200-36389200	Weak transcription	Right Atrium	heart
4	chr19:36362400-36378200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:36362600-36378000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr19:36366000-36378200	Weak transcription	Gastric	stomach
7	chr19:36367800-36378400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:36370400-36379000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:36370400-36379200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:36370600-36379000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:36370600-36379000	Weak transcription	NHDF-Ad	bronchial
12	chr19:36370600-36389000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:36370800-36378000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr19:36370800-36378000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:36370800-36378200	Weak transcription	Fetal Intestine Large	intestine
16	chr19:36370800-36378200	Weak transcription	Fetal Intestine Small	intestine
17	chr19:36370800-36378200	Weak transcription	Lung	lung
18	chr19:36370800-36378200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr19:36370800-36378400	Weak transcription	Placenta	Placenta
20	chr19:36370800-36378400	Weak transcription	GM12878-XiMat	blood
21	chr19:36370800-36378800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:36370800-36378800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr19:36370800-36378800	Weak transcription	Stomach Mucosa	stomach
24	chr19:36370800-36378800	Weak transcription	Dnd41	blood
25	chr19:36370800-36379000	Weak transcription	Liver	Liver
26	chr19:36370800-36379000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr19:36370800-36379000	Weak transcription	Fetal Lung	lung
28	chr19:36370800-36379400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr19:36370800-36389200	Weak transcription	HSMM	muscle
30	chr19:36370800-36389400	Weak transcription	HUVEC	blood vessel
31	chr19:36370800-36389400	Weak transcription	NH-A	brain
32	chr19:36371000-36378000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr19:36371000-36378000	Weak transcription	Brain Anterior Caudate	brain
34	chr19:36371000-36378000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr19:36371000-36378000	Weak transcription	Thymus	Thymus
36	chr19:36371000-36378200	Weak transcription	Esophagus	oesophagus
37	chr19:36371000-36378200	Weak transcription	HSMMtube	muscle
38	chr19:36371000-36378800	Weak transcription	Pancreas	Pancrea
39	chr19:36371000-36379000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:36371200-36378000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr19:36371200-36378200	Weak transcription	Hela-S3	cervix
42	chr19:36371200-36378800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr19:36371200-36378800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:36371200-36379000	Weak transcription	Fetal Muscle Leg	muscle
45	chr19:36371200-36380400	Weak transcription	Brain Substantia Nigra	brain
46	chr19:36371200-36380400	Weak transcription	K562	blood
47	chr19:36371200-36380800	Weak transcription	Brain Germinal Matrix	brain
48	chr19:36371800-36378200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr19:36372600-36378000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr19:36372600-36378000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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