Variant report

Variant	rs7749100
Chromosome Location	chr6:56529237-56529238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56528887..56533842-chr6:56534833..56537756,4	MCF-7	breast:
2	chr6:56489382..56492245-chr6:56527517..56529634,2	MCF-7	breast:
3	chr6:56505768..56508358-chr6:56526812..56530016,3	MCF-7	breast:
4	chr6:56528704..56530414-chr6:56552846..56555109,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1024196	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.85[MKK][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11961141	0.89[ASN][1000 genomes]
rs11961342	1.00[ASN][1000 genomes]
rs11963288	0.94[EUR][1000 genomes]
rs11966986	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11967796	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968575	1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs11970410	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11970648	1.00[CHD][hapmap]
rs13191164	1.00[ASN][1000 genomes]
rs13192478	0.89[ASN][1000 genomes]
rs13192567	0.89[ASN][1000 genomes]
rs13205013	1.00[ASN][1000 genomes]
rs13210876	0.89[ASN][1000 genomes]
rs13213878	0.89[ASN][1000 genomes]
rs13219546	0.89[ASN][1000 genomes]
rs1407831	0.89[EUR][1000 genomes]
rs1535609	0.94[EUR][1000 genomes]
rs1535611	0.94[EUR][1000 genomes]
rs16887928	0.89[EUR][1000 genomes]
rs16888070	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16888085	0.90[ASN][1000 genomes]
rs16888096	1.00[ASN][1000 genomes]
rs16888106	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888118	1.00[ASN][1000 genomes]
rs16888124	1.00[ASN][1000 genomes]
rs16888128	1.00[ASN][1000 genomes]
rs16888130	1.00[ASN][1000 genomes]
rs16888133	1.00[ASN][1000 genomes]
rs16888135	0.89[ASN][1000 genomes]
rs16888171	1.00[CHD][hapmap]
rs1903332	1.00[CHD][hapmap]
rs2144407	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2180148	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207678	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2397224	0.89[EUR][1000 genomes]
rs28633631	1.00[EUR][1000 genomes]
rs2967960	0.89[ASN][1000 genomes]
rs3002003	0.89[ASN][1000 genomes]
rs3002004	0.89[ASN][1000 genomes]
rs34138864	0.90[ASN][1000 genomes]
rs34429594	1.00[ASN][1000 genomes]
rs34724718	1.00[ASN][1000 genomes]
rs34812826	0.89[ASN][1000 genomes]
rs34824960	0.89[ASN][1000 genomes]
rs35089136	0.89[ASN][1000 genomes]
rs35206656	1.00[ASN][1000 genomes]
rs35637749	1.00[ASN][1000 genomes]
rs35687635	1.00[ASN][1000 genomes]
rs35920751	0.89[ASN][1000 genomes]
rs36068365	1.00[ASN][1000 genomes]
rs3800026	0.94[EUR][1000 genomes]
rs3924307	0.94[EUR][1000 genomes]
rs4072271	1.00[ASN][1000 genomes]
rs41267673	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271848	0.89[EUR][1000 genomes]
rs41271850	0.89[EUR][1000 genomes]
rs41271854	0.94[EUR][1000 genomes]
rs41271856	0.94[EUR][1000 genomes]
rs41271872	1.00[EUR][1000 genomes]
rs41271876	1.00[EUR][1000 genomes]
rs41271878	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4133076	1.00[ASN][1000 genomes]
rs4256439	0.94[EUR][1000 genomes]
rs4275049	0.89[ASN][1000 genomes]
rs4288197	0.84[EUR][1000 genomes]
rs45442999	0.94[EUR][1000 genomes]
rs45553042	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4574644	0.89[ASN][1000 genomes]
rs4640889	0.89[ASN][1000 genomes]
rs56094263	0.89[ASN][1000 genomes]
rs56196625	1.00[ASN][1000 genomes]
rs56991168	0.81[EUR][1000 genomes]
rs57289287	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57350484	1.00[EUR][1000 genomes]
rs57392123	1.00[ASN][1000 genomes]
rs57488435	1.00[ASN][1000 genomes]
rs57790896	1.00[EUR][1000 genomes]
rs57822928	0.94[EUR][1000 genomes]
rs58487319	0.81[EUR][1000 genomes]
rs58565063	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58730144	0.94[EUR][1000 genomes]
rs59073430	1.00[ASN][1000 genomes]
rs59085778	0.89[ASN][1000 genomes]
rs59162324	0.89[ASN][1000 genomes]
rs59247267	0.89[ASN][1000 genomes]
rs59772940	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59864125	0.94[EUR][1000 genomes]
rs59889120	1.00[ASN][1000 genomes]
rs60360551	1.00[ASN][1000 genomes]
rs60498201	0.89[ASN][1000 genomes]
rs62621210	0.94[EUR][1000 genomes]
rs6459167	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6459168	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900572	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901176	1.00[ASN][1000 genomes]
rs6903517	0.85[EUR][1000 genomes]
rs6903815	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916813	1.00[ASN][1000 genomes]
rs6924375	1.00[ASN][1000 genomes]
rs6926134	0.89[ASN][1000 genomes]
rs6941626	1.00[EUR][1000 genomes]
rs73455767	0.94[EUR][1000 genomes]
rs73455782	0.94[EUR][1000 genomes]
rs73455797	0.81[EUR][1000 genomes]
rs73465854	0.94[EUR][1000 genomes]
rs73746926	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73746929	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73746930	1.00[ASN][1000 genomes]
rs73746931	1.00[ASN][1000 genomes]
rs73747826	0.89[EUR][1000 genomes]
rs73747832	0.89[EUR][1000 genomes]
rs73749935	0.94[EUR][1000 genomes]
rs73749942	0.94[EUR][1000 genomes]
rs73749948	0.94[EUR][1000 genomes]
rs73749949	0.94[EUR][1000 genomes]
rs7749437	1.00[ASN][1000 genomes]
rs7758867	1.00[CHD][hapmap]
rs7759479	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760503	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760515	1.00[CEU][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7760542	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760701	1.00[EUR][1000 genomes]
rs7761027	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767128	1.00[ASN][1000 genomes]
rs7769014	0.94[EUR][1000 genomes]
rs7775134	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.81[AFR][1000 genomes];1.00[EUR][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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv432888	chr6:56507489-56560764	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr6:56480800-56536400	Weak transcription	Gastric	stomach
2	chr6:56491600-56536600	Weak transcription	Fetal Brain Female	brain
3	chr6:56505600-56537400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:56512600-56534400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr6:56513000-56534400	Weak transcription	Fetal Muscle Leg	muscle
6	chr6:56514800-56537000	Weak transcription	Lung	lung
7	chr6:56515000-56534400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:56517400-56536400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:56521000-56536600	Weak transcription	Fetal Stomach	stomach
10	chr6:56521200-56532800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:56521200-56536400	Weak transcription	Right Ventricle	heart
12	chr6:56521400-56534400	Weak transcription	NHLF	lung
13	chr6:56522000-56535000	Weak transcription	HUVEC	blood vessel
14	chr6:56522000-56536400	Weak transcription	Adipose Nuclei	Adipose
15	chr6:56523600-56531800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:56524800-56534400	Weak transcription	HSMMtube	muscle
17	chr6:56524800-56536400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:56525200-56531400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:56525200-56532000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:56525200-56532200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:56525200-56534600	Weak transcription	Thymus	Thymus
22	chr6:56525200-56534800	Weak transcription	Left Ventricle	heart
23	chr6:56525200-56535400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:56525200-56536000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:56525400-56536400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr6:56525600-56534400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:56525800-56530600	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:56526400-56533000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:56526400-56536200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:56526400-56536600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:56526400-56540400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:56526400-56549200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:56526600-56531000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:56526800-56531200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr6:56526800-56531200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:56526800-56534400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:56526800-56537000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr6:56527000-56532800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr6:56527000-56536600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr6:56527000-56554400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr6:56527200-56529400	Enhancers	Brain Hippocampus Middle	brain
42	chr6:56527400-56536600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:56527600-56529400	Enhancers	Fetal Intestine Large	intestine
44	chr6:56527600-56530000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:56527800-56529400	Enhancers	Fetal Lung	lung
46	chr6:56527800-56529400	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr6:56527800-56530000	Enhancers	Brain Substantia Nigra	brain
48	chr6:56527800-56530600	Enhancers	A549	lung
49	chr6:56527800-56531600	Weak transcription	Fetal Thymus	thymus
50	chr6:56528000-56529400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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