Variant report

Variant	rs6807137
Chromosome Location	chr3:99831799-99831800
allele	A/C
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	GATA3	chr3:99831529-99832506	MCF-7	breast:	n/a	chr3:99832290-99832297 chr3:99832283-99832304
2	ZNF217	chr3:99831629-99832020	MCF-7	breast:	n/a	n/a
3	GATA3	chr3:99831330-99832202	MCF-7	breast:	n/a	n/a
4	GATA3	chr3:99831617-99831959	MCF-7	breast:	n/a	n/a
5	SIN3AK20	chr3:99831601-99832585	MCF-7	breast:	n/a	n/a
6	GATA3	chr3:99831608-99832538	MCF-7	breast:	n/a	chr3:99832290-99832297 chr3:99832283-99832304

No.	Distal block	Cell Line	Cell type
1	chr3:99826246..99828968-chr3:99829999..99832998,3	K562	blood:
2	chr3:99829927..99832057-chr3:99833364..99835839,2	K562	blood:
3	chr3:99826432..99828172-chr3:99830393..99831997,2	K562	blood:
4	chr3:99824566..99827105-chr3:99830597..99832323,2	MCF-7	breast:

Variant related genes	Relation type
CMSS1	TF binding region
ENSG00000184220	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs16842034	1.00[EUR][1000 genomes]
rs17313676	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17314245	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17314280	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17314977	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17338576	1.00[EUR][1000 genomes]
rs17392822	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17393080	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17397949	1.00[EUR][1000 genomes]
rs17779605	1.00[EUR][1000 genomes]
rs41272629	1.00[EUR][1000 genomes]
rs41272631	1.00[EUR][1000 genomes]
rs41272633	1.00[EUR][1000 genomes]
rs41444055	1.00[YRI][hapmap]
rs62636640	1.00[EUR][1000 genomes]
rs62636641	1.00[EUR][1000 genomes]
rs6762809	1.00[EUR][1000 genomes]
rs6762871	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6764470	1.00[YRI][hapmap]
rs6768684	1.00[EUR][1000 genomes]
rs6778756	1.00[YRI][hapmap]
rs6781780	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6784150	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787184	1.00[YRI][hapmap]
rs6788807	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6789840	1.00[YRI][hapmap]
rs6790187	1.00[EUR][1000 genomes]
rs6791426	1.00[YRI][hapmap]
rs6794130	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6794365	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6801514	1.00[YRI][hapmap]
rs6805834	1.00[YRI][hapmap]
rs6807615	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs72936590	0.83[EUR][1000 genomes]
rs7611313	1.00[EUR][1000 genomes]
rs7612083	1.00[YRI][hapmap]
rs7612089	1.00[YRI][hapmap]
rs7619738	1.00[EUR][1000 genomes]
rs7626214	1.00[YRI][hapmap]
rs7626310	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs7628458	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7637974	1.00[YRI][hapmap]
rs7646221	1.00[EUR][1000 genomes]
rs7648943	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7652596	1.00[EUR][1000 genomes]
rs766777	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs768527	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99795800-99866600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99818000-99836600	Weak transcription	Primary B cells from cord blood	blood
3	chr3:99823600-99837200	Weak transcription	Pancreas	Pancrea
4	chr3:99825200-99835000	Weak transcription	K562	blood
5	chr3:99825200-99840600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:99825200-99844000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:99825200-99844200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:99825600-99841000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:99826000-99833200	Weak transcription	Ovary	ovary
10	chr3:99826200-99838200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:99826400-99832000	Weak transcription	Right Ventricle	heart
12	chr3:99826600-99862600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:99827400-99839000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:99827800-99832000	Weak transcription	Left Ventricle	heart
15	chr3:99827800-99833000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:99827800-99834200	Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr3:99828000-99832200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:99828400-99833000	Weak transcription	HepG2	liver
19	chr3:99829200-99833200	Active TSS	Right Atrium	heart
20	chr3:99829200-99841000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:99829400-99833400	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr3:99829800-99833200	Weak transcription	Aorta	Aorta
23	chr3:99830000-99832600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:99830000-99841200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:99830400-99833000	Active TSS	Fetal Muscle Leg	muscle
26	chr3:99831000-99833200	Active TSS	Fetal Muscle Trunk	muscle
27	chr3:99831400-99832200	Weak transcription	Psoas Muscle	Psoas
28	chr3:99831400-99833600	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:99831400-99841400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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