Variant report

Variant	rs9399678
Chromosome Location	chr6:149354307-149354308
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	TCF7L2	chr6:149354037-149354533	HCT-116	colon:	n/a	n/a
2	EP300	chr6:149353633-149354949	GM12878	blood:	n/a	chr6:149354049-149354063
3	BCL11A	chr6:149353700-149354352	GM12878	blood:	n/a	chr6:149353941-149353950
4	POLR2A	chr6:149352419-149354573	U87	brain:	n/a	n/a
5	BHLHE40	chr6:149353074-149354942	GM12878	blood:	n/a	chr6:149353322-149353338
6	FOSL2	chr6:149352679-149354751	A549	lung:	n/a	chr6:149354124-149354134 chr6:149353283-149353293 chr6:149354457-149354465 chr6:149354544-149354555 chr6:149353283-149353293 chr6:149354457-149354464 chr6:149354124-149354134 chr6:149353283-149353293 chr6:149353284-149353292 chr6:149353283-149353293
7	MEF2A	chr6:149353574-149355007	GM12878	blood:	n/a	chr6:149354238-149354253 chr6:149354482-149354496
8	MAFK	chr6:149353899-149354642	HepG2	liver:	n/a	chr6:149354457-149354467 chr6:149354460-149354471 chr6:149354458-149354467
9	RCOR1	chr6:149352928-149355080	GM12878	blood:	n/a	n/a
10	FOXM1	chr6:149353279-149355039	GM12878	blood:	n/a	n/a
11	EP300	chr6:149354012-149354475	MCF-7	breast:	n/a	chr6:149354049-149354063
12	NR3C1	chr6:149354054-149354504	A549	lung:	n/a	chr6:149354255-149354273 chr6:149354251-149354277 chr6:149354251-149354277 chr6:149354251-149354277 chr6:149354253-149354274
13	WRNIP1	chr6:149352864-149354407	GM12878	blood:	n/a	n/a
14	RUNX3	chr6:149353036-149354920	GM12878	blood:	n/a	n/a
15	JUND	chr6:149353961-149354615	HepG2	liver:	n/a	chr6:149354124-149354134 chr6:149354457-149354465 chr6:149354544-149354555 chr6:149354457-149354464 chr6:149354124-149354134
16	MEF2A	chr6:149352971-149354679	SK-N-SH	brain:	n/a	chr6:149354238-149354253 chr6:149354482-149354496
17	BCL3	chr6:149353055-149354693	A549	lung:	n/a	chr6:149353941-149353950
18	RUNX3	chr6:149352788-149355044	GM12878	blood:	n/a	n/a
19	FOS	chr6:149353771-149354670	MCF10A-Er-Src	breast:	n/a	chr6:149354124-149354134 chr6:149354457-149354465 chr6:149354544-149354555 chr6:149354457-149354464 chr6:149354124-149354134
20	SMC3	chr6:149353628-149354399	GM12878	blood:	n/a	n/a
21	RAD21	chr6:149353829-149354427	IMR90	lung:	n/a	n/a
22	SMC3	chr6:149352814-149354515	Hela-S3	cervix:	n/a	n/a
23	FOS	chr6:149353772-149354622	MCF10A-Er-Src	breast:	n/a	chr6:149354124-149354134 chr6:149354457-149354465 chr6:149354544-149354555 chr6:149354457-149354464 chr6:149354124-149354134
24	POU2F2	chr6:149352871-149354523	GM12878	blood:	n/a	n/a
25	ESR1	chr6:149354082-149354391	T-47D	breast:	n/a	n/a
26	NFIC	chr6:149353446-149354966	GM12878	blood:	n/a	chr6:149354369-149354386 chr6:149354369-149354385
27	NR2F2	chr6:149352313-149354512	MCF-7	breast:	n/a	n/a
28	MAFK	chr6:149352911-149354809	Hela-S3	cervix:	n/a	chr6:149354457-149354467 chr6:149354460-149354471 chr6:149354458-149354467
29	CEBPB	chr6:149353735-149354793	Hela-S3	cervix:	n/a	n/a
30	STAT5A	chr6:149352729-149354965	GM12878	blood:	n/a	chr6:149353461-149353469 chr6:149352925-149352937 chr6:149354815-149354827 chr6:149353941-149353950
31	POLR2A	chr6:149352552-149354568	U87	brain:	n/a	n/a
32	ESR1	chr6:149354059-149354474	T-47D	breast:	n/a	n/a
33	FOXA2	chr6:149353735-149354477	A549	lung:	n/a	n/a
34	IRF4	chr6:149353505-149354546	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:149352841-149354425	GM18505	blood:	n/a	n/a
36	POLR2A	chr6:149354179-149354564	MCF10A-Er-Src	breast:	n/a	n/a
37	JUND	chr6:149352905-149354707	SK-N-SH	brain:	n/a	chr6:149354124-149354134 chr6:149353283-149353293 chr6:149354457-149354465 chr6:149354544-149354555 chr6:149353283-149353293 chr6:149354457-149354464 chr6:149354124-149354134 chr6:149353283-149353293 chr6:149353284-149353292 chr6:149353283-149353293
38	PBX3	chr6:149352939-149354744	SK-N-SH	brain:	n/a	n/a
39	TAF1	chr6:149354191-149354462	SK-N-SH	brain:	n/a	n/a
40	PAX5	chr6:149353866-149354341	GM12891	blood:	n/a	n/a
41	MBD4	chr6:149354019-149354609	HepG2	liver:	n/a	n/a
42	RELA	chr6:149353445-149354947	GM12891	blood:	n/a	n/a
43	RELA	chr6:149353750-149354932	GM10847	blood:	n/a	n/a
44	CHD2	chr6:149353762-149354530	Hela-S3	cervix:	n/a	n/a
45	TCF12	chr6:149352903-149354804	SK-N-SH	brain:	n/a	chr6:149353533-149353543
46	EP300	chr6:149354256-149354604	SK-N-SH_RA	brain:	n/a	n/a
47	GATA3	chr6:149353629-149354394	MCF-7	breast:	n/a	n/a
48	TCF12	chr6:149352812-149354813	SK-N-SH	brain:	n/a	chr6:149353533-149353543
49	FOS	chr6:149353787-149354612	MCF10A-Er-Src	breast:	n/a	chr6:149354124-149354134 chr6:149354457-149354465 chr6:149354544-149354555 chr6:149354457-149354464 chr6:149354124-149354134
50	GATA3	chr6:149352096-149354563	MCF-7	breast:	n/a	chr6:149353285-149353294 chr6:149352510-149352519

No.	Distal block	Cell Line	Cell type
1	chr6:149354185..149354797-chr6:149399693..149400514,2	MCF-7	breast:
2	chr6:149353945..149354680-chr6:149401078..149401622,2	MCF-7	breast:
3	chr6:149351823..149355344-chr6:149638842..149641991,4	MCF-7	breast:
4	chr6:149352653..149356079-chr6:149835245..149838856,4	MCF-7	breast:
5	chr6:149351574..149354764-chr6:149837931..149839815,3	MCF-7	breast:
6	chr6:149353980..149354853-chr6:149401096..149401673,2	MCF-7	breast:
7	chr6:149353741..149354649-chr6:149401105..149401931,5	MCF-7	breast:
8	chr6:149353960..149356786-chr6:149766378..149768113,2	MCF-7	breast:
9	chr6:149353899..149354712-chr6:149398410..149398949,2	MCF-7	breast:
10	chr6:149352728..149354619-chr6:150038400..150040013,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236591	TF binding region
ENSG00000055208	Chromatin interaction
ENSG00000131023	Chromatin interaction
ENSG00000131013	Chromatin interaction
ENSG00000252244	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10457074	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1317171	0.80[AMR][1000 genomes]
rs2275423	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2340751	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2340752	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2340801	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2340802	0.82[CHB][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2486409	0.83[CEU][hapmap]
rs2486411	0.82[CEU][hapmap]
rs2500549	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs2879843	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4318907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4377808	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4897074	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4897076	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6570920	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6904550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911303	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs6930989	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6931744	0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6936176	0.80[CEU][hapmap];0.83[AMR][1000 genomes]
rs7747463	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7748978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7765778	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7774457	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7774887	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7776117	0.80[AMR][1000 genomes]
rs9377187	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9377188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149305400-149381400	Weak transcription	Gastric	stomach
2	chr6:149336200-149358000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:149337600-149358000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:149339400-149364600	Weak transcription	Lung	lung
5	chr6:149341000-149365400	Weak transcription	Right Ventricle	heart
6	chr6:149343200-149358000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr6:149344000-149357200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:149344000-149357400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr6:149344600-149357800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:149344800-149354800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:149344800-149358000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:149345000-149355200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:149345400-149362000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:149345600-149355000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:149345600-149358000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:149347800-149356800	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:149348000-149367400	Weak transcription	Primary B cells from cord blood	blood
18	chr6:149349800-149354400	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr6:149349800-149354800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:149350200-149357600	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:149350400-149358000	Weak transcription	Fetal Kidney	kidney
22	chr6:149351800-149354800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:149351800-149355000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:149351800-149355400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:149352000-149354800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:149352400-149354800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:149352400-149354800	Enhancers	Liver	Liver
28	chr6:149352400-149355200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:149352400-149355200	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr6:149352400-149355600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:149352600-149355200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr6:149352800-149354800	Flanking Active TSS	NH-A	brain
33	chr6:149352800-149354800	Enhancers	NHLF	lung
34	chr6:149352800-149354800	Flanking Active TSS	Osteobl	bone
35	chr6:149352800-149355000	Enhancers	Primary hematopoietic stem cells	blood
36	chr6:149352800-149355000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:149352800-149355600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr6:149352800-149355800	Enhancers	Fetal Lung	lung
39	chr6:149353000-149354400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr6:149353000-149354400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:149353000-149354400	Flanking Active TSS	HSMM	muscle
42	chr6:149353000-149354800	Enhancers	HMEC	breast
43	chr6:149353000-149355200	Enhancers	NHDF-Ad	bronchial
44	chr6:149353000-149355800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:149353000-149355800	Enhancers	Ovary	ovary
46	chr6:149353200-149354800	Enhancers	Primary B cells from peripheral blood	blood
47	chr6:149353200-149354800	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr6:149353400-149354400	Enhancers	Primary T cells fromperipheralblood	blood
49	chr6:149353400-149354400	Enhancers	Adipose Nuclei	Adipose
50	chr6:149353400-149354400	Enhancers	Brain Substantia Nigra	brain

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