Variant report

Variant	rs9878950
Chromosome Location	chr3:48608506-48608507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48608242-48609279	A549	lung:	n/a	n/a
2	POLR2A	chr3:48608265-48610615	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48598407..48599969-chr3:48607969..48610789,2	K562	blood:
2	chr3:48603206..48606480-chr3:48608320..48612943,6	K562	blood:
3	chr3:48601397..48603456-chr3:48607789..48610015,2	MCF-7	breast:

Variant related genes	Relation type
COL7A1	TF binding region
ENSG00000114270	Chromatin interaction
ENSG00000114268	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1003649	0.86[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs10470687	0.87[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11706983	0.83[GIH][hapmap]
rs11708786	0.83[GIH][hapmap]
rs11719291	0.83[GIH][hapmap]
rs12107252	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs12107418	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13060933	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13063312	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13070798	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13091944	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13094578	0.81[ASN][1000 genomes]
rs13100178	0.81[ASN][1000 genomes]
rs13319635	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13319651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324142	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13434258	0.83[GIH][hapmap]
rs17080289	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.85[ASN][1000 genomes]
rs2006871	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2255532	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs2276850	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2276852	0.80[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2286652	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2302295	1.00[JPT][hapmap]
rs2310996	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2854394	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2854395	0.94[ASN][1000 genomes]
rs28563843	0.94[ASN][1000 genomes]
rs28581474	0.92[ASN][1000 genomes]
rs34107861	0.85[CHD][hapmap]
rs35064573	0.83[GIH][hapmap]
rs35343040	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35562294	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35796820	0.85[ASN][1000 genomes]
rs3755819	0.98[ASN][1000 genomes]
rs3806694	1.00[JPT][hapmap]
rs3821875	1.00[JPT][hapmap]
rs3821876	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs3969942	0.85[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs4075082	0.81[ASN][1000 genomes]
rs6773261	1.00[JPT][hapmap]
rs6781283	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6792156	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs6792525	0.87[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs6806059	0.86[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.92[ASN][1000 genomes]
rs740787	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7428949	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7434077	0.80[CHD][hapmap];0.81[ASN][1000 genomes]
rs7434107	0.81[ASN][1000 genomes]
rs7620853	1.00[JPT][hapmap]
rs7623614	0.81[ASN][1000 genomes]
rs7631574	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7640031	0.81[ASN][1000 genomes]
rs7644771	0.81[ASN][1000 genomes]
rs9810549	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9810991	0.87[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.94[ASN][1000 genomes]
rs9811318	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9812200	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9814951	0.80[CHB][hapmap];0.85[GIH][hapmap]
rs9816942	0.81[ASN][1000 genomes]
rs9821797	1.00[JPT][hapmap]
rs9830581	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9835902	0.85[GIH][hapmap]
rs9836462	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9837687	0.87[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.94[ASN][1000 genomes]
rs9841602	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9843316	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9848824	0.94[ASN][1000 genomes]
rs9849280	0.94[ASN][1000 genomes]
rs9850102	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9851743	0.81[ASN][1000 genomes]
rs9851771	0.80[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs9864729	0.94[ASN][1000 genomes]
rs9869698	0.87[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.94[ASN][1000 genomes]
rs9871180	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9871608	0.81[ASN][1000 genomes]
rs9873726	1.00[JPT][hapmap]
rs9875911	1.00[GIH][hapmap]
rs9881877	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9882549	0.83[GIH][hapmap]
rs9882962	0.85[CHD][hapmap];1.00[GIH][hapmap];0.85[ASN][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	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv3811	chr3:48599180-48643809	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48596600-48626000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:48598600-48624000	Weak transcription	Aorta	Aorta
3	chr3:48598800-48609000	Weak transcription	Esophagus	oesophagus
4	chr3:48598800-48615000	Weak transcription	Pancreas	Pancrea
5	chr3:48598800-48617200	Weak transcription	Brain Germinal Matrix	brain
6	chr3:48599000-48614800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:48599000-48623600	Weak transcription	Ovary	ovary
8	chr3:48599000-48632000	Weak transcription	Left Ventricle	heart
9	chr3:48599200-48616800	Weak transcription	Fetal Heart	heart
10	chr3:48599200-48630600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:48600600-48631800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:48601000-48631000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:48601200-48616800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:48601400-48614400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:48601600-48609400	Strong transcription	Fetal Intestine Small	intestine
16	chr3:48601600-48631000	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:48601800-48608600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:48601800-48613400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:48601800-48613600	Weak transcription	Brain Anterior Caudate	brain
20	chr3:48601800-48614200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:48601800-48614600	Weak transcription	Brain Substantia Nigra	brain
22	chr3:48601800-48614800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:48601800-48617000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:48601800-48633000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:48602000-48614400	Weak transcription	Spleen	Spleen
26	chr3:48602000-48614600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:48602000-48619400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:48602000-48629400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:48602000-48633200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:48602200-48629400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:48602400-48621400	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:48603200-48609200	Enhancers	HepG2	liver
33	chr3:48603600-48613400	Weak transcription	Brain Angular Gyrus	brain
34	chr3:48603600-48630000	Strong transcription	Fetal Stomach	stomach
35	chr3:48603800-48613400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr3:48603800-48628800	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr3:48603800-48630600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:48603800-48631800	Weak transcription	Gastric	stomach
39	chr3:48604000-48608600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:48604000-48608800	Weak transcription	Placenta	Placenta
41	chr3:48604000-48611200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:48604000-48611800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:48604000-48614000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:48604000-48614600	Weak transcription	Osteobl	bone
45	chr3:48604000-48623800	Weak transcription	Fetal Muscle Leg	muscle
46	chr3:48604000-48629400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:48604000-48631600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:48604000-48632000	Weak transcription	HSMMtube	muscle
49	chr3:48604200-48614600	Weak transcription	NHDF-Ad	bronchial
50	chr3:48604200-48621600	Weak transcription	Muscle Satellite Cultured Cells	--

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