Variant report

Variant	rs9843316
Chromosome Location	chr3:48635680-48635681
allele	A/G
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	FOSL2	chr3:48635581-48636373	SK-N-SH	brain:	n/a	chr3:48635895-48635907 chr3:48635893-48635904 chr3:48635896-48635907 chr3:48636348-48636359 chr3:48635896-48635906
2	POLR2A	chr3:48633989-48635733	K562	blood:	n/a	n/a
3	TCF12	chr3:48635552-48636626	SK-N-SH	brain:	n/a	chr3:48636197-48636207 chr3:48636201-48636208 chr3:48636124-48636132
4	POLR2A	chr3:48633186-48635705	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:48632952-48636594	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr3:48630527-48636597	U87	brain:	n/a	n/a
7	MEF2A	chr3:48635640-48636332	SK-N-SH	brain:	n/a	chr3:48635880-48635895
8	TCF12	chr3:48635480-48636537	A549	lung:	n/a	chr3:48636197-48636207 chr3:48636201-48636208 chr3:48636124-48636132
9	POLR2A	chr3:48635661-48635680	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr3:48635639-48636146	Hela-S3	cervix:	n/a	n/a
11	SP1	chr3:48635599-48636540	A549	lung:	n/a	chr3:48635846-48635860 chr3:48635849-48635861
12	POLR2A	chr3:48635573-48636571	U87	brain:	n/a	n/a
13	POLR2A	chr3:48633205-48636402	K562	blood:	n/a	n/a
14	POLR2A	chr3:48633854-48635968	K562	blood:	n/a	n/a
15	POLR2A	chr3:48634812-48635771	K562	blood:	n/a	n/a
16	MEF2A	chr3:48635584-48636481	SK-N-SH	brain:	n/a	chr3:48635880-48635895
17	GATA3	chr3:48635584-48636523	A549	lung:	n/a	chr3:48635731-48635747 chr3:48635736-48635747 chr3:48635729-48635750
18	MEF2A	chr3:48635648-48636055	K562	blood:	n/a	chr3:48635880-48635895
19	POLR2A	chr3:48633904-48636248	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAFK	chr3:48635614-48636478	IMR90	lung:	n/a	chr3:48635898-48635907
21	POLR2A	chr3:48632955-48636737	K562	blood:	n/a	n/a
22	POLR2A	chr3:48635596-48636458	IMR90	lung:	n/a	n/a
23	POLR2A	chr3:48634390-48636338	K562	blood:	n/a	n/a
24	TCF12	chr3:48635667-48636548	SK-N-SH	brain:	n/a	chr3:48636197-48636207 chr3:48636201-48636208 chr3:48636124-48636132
25	MAZ	chr3:48635228-48636970	IMR90	lung:	n/a	chr3:48635850-48635860
26	POLR2A	chr3:48631733-48636361	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr3:48634430-48635718	GM12892	blood:	n/a	n/a
28	POLR2A	chr3:48632891-48636301	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48633143..48634875-chr3:48635486..48637467,3	MCF-7	breast:
2	chr3:48634266..48637382-chr3:48644809..48648389,6	MCF-7	breast:
3	chr3:48634135..48636192-chr3:48639915..48641521,2	MCF-7	breast:
4	chr3:48634983..48637282-chr3:48645577..48648771,3	K562	blood:
5	chr3:48634898..48636803-chr3:48686799..48688357,2	MCF-7	breast:
6	chr3:48633231..48638086-chr3:48639417..48644972,8	MCF-7	breast:
7	chr3:48635113..48637147-chr3:48645892..48647731,2	MCF-7	breast:
8	chr3:48633338..48635832-chr3:48883442..48885792,2	K562	blood:
9	chr3:48634045..48636244-chr3:48672323..48674117,3	MCF-7	breast:
10	chr3:48631354..48634791-chr3:48635080..48639274,6	MCF-7	breast:
11	chr3:48634583..48638851-chr3:48666607..48670894,4	MCF-7	breast:
12	chr3:48624465..48626090-chr3:48634843..48637573,2	K562	blood:

Variant related genes	Relation type
COL7A1	TF binding region
ENSG00000225697	Chromatin interaction
ENSG00000114270	Chromatin interaction
ENSG00000010256	Chromatin interaction
ENSG00000114302	Chromatin interaction
ENSG00000224424	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1003649	1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap]
rs10470687	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11706983	1.00[GIH][hapmap]
rs11708786	1.00[GIH][hapmap]
rs11713694	0.83[GIH][hapmap]
rs11719291	1.00[GIH][hapmap]
rs12107252	0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12107418	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs13060933	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13063312	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13070798	0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs13074318	0.83[GIH][hapmap]
rs13076269	0.81[ASN][1000 genomes]
rs13091944	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13096357	0.81[ASN][1000 genomes]
rs13319635	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13319651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13324142	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13434258	1.00[GIH][hapmap]
rs17080289	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2006871	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs2255532	0.82[CHB][hapmap]
rs2276850	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2276852	0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2286652	0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2302295	1.00[JPT][hapmap]
rs2310996	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2310997	0.81[ASN][1000 genomes]
rs2854394	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2854395	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28563843	0.80[ASN][1000 genomes]
rs28581474	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34037363	0.83[GIH][hapmap]
rs34107861	0.80[CHD][hapmap]
rs34368826	0.83[ASN][1000 genomes]
rs35064573	1.00[GIH][hapmap]
rs35343040	1.00[ASN][1000 genomes]
rs35562294	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35796820	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3755819	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3806694	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3821875	1.00[JPT][hapmap]
rs3821876	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3969942	0.85[CHD][hapmap];0.83[GIH][hapmap]
rs57334642	0.83[ASN][1000 genomes]
rs6773261	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6781283	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6792156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6792525	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6806059	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs740787	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7428949	1.00[JPT][hapmap]
rs7620853	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7631574	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9810549	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9810991	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.80[ASN][1000 genomes]
rs9811318	0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9812200	0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9814951	0.80[CHB][hapmap]
rs9821797	1.00[JPT][hapmap]
rs9830581	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836462	0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9837687	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9841602	0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9848824	0.80[ASN][1000 genomes]
rs9849280	0.80[ASN][1000 genomes]
rs9850102	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9851771	0.83[GIH][hapmap]
rs9864729	0.80[ASN][1000 genomes]
rs9868809	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs9869698	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9871180	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9873726	1.00[JPT][hapmap]
rs9875911	0.83[GIH][hapmap]
rs9878063	0.83[ASN][1000 genomes]
rs9878950	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]
rs9881877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[ASN][1000 genomes]
rs9882549	1.00[GIH][hapmap]
rs9882962	0.81[CHD][hapmap];0.83[GIH][hapmap]

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	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
7	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48631800-48636000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr3:48631800-48637000	Enhancers	Fetal Heart	heart
3	chr3:48632400-48638600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:48632600-48636000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr3:48632600-48636400	Weak transcription	Brain Angular Gyrus	brain
6	chr3:48632600-48639000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:48632800-48637000	Enhancers	Esophagus	oesophagus
8	chr3:48632800-48639200	Enhancers	Right Atrium	heart
9	chr3:48633000-48637400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:48633200-48636200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:48633200-48637000	Enhancers	Placenta Amnion	Placenta Amnion
12	chr3:48633200-48637400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr3:48633400-48637400	Weak transcription	HUVEC	blood vessel
14	chr3:48633400-48638400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:48633600-48636000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:48633600-48636600	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr3:48633600-48637400	Genic enhancers	Fetal Stomach	stomach
18	chr3:48633800-48640600	Weak transcription	Fetal Brain Male	brain
19	chr3:48634000-48636200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:48634000-48636600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr3:48634000-48637000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:48634000-48637400	Genic enhancers	A549	lung
23	chr3:48634000-48642400	Strong transcription	Fetal Brain Female	brain
24	chr3:48634200-48636000	Strong transcription	Fetal Intestine Small	intestine
25	chr3:48634200-48636000	Genic enhancers	HMEC	breast
26	chr3:48634200-48637800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:48634200-48637800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:48634200-48638400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:48634200-48639000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:48634200-48644200	Strong transcription	Brain Germinal Matrix	brain
31	chr3:48634200-48644600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:48634200-48646200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr3:48634400-48636400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
34	chr3:48634400-48637000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:48634400-48637000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr3:48634400-48637600	Genic enhancers	NHLF	lung
37	chr3:48634400-48643400	Strong transcription	Primary B cells from cord blood	blood
38	chr3:48634400-48643600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:48634600-48636200	Enhancers	Psoas Muscle	Psoas
40	chr3:48634600-48636600	Genic enhancers	Lung	lung
41	chr3:48634600-48637400	Genic enhancers	Fetal Muscle Leg	muscle
42	chr3:48634600-48638000	Genic enhancers	Fetal Muscle Trunk	muscle
43	chr3:48634600-48639400	Genic enhancers	Right Ventricle	heart
44	chr3:48634600-48644000	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr3:48634600-48644400	Strong transcription	Primary T cells from cord blood	blood
46	chr3:48634600-48645200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr3:48634600-48645200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr3:48634600-48645600	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr3:48634600-48645600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:48634600-48645600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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