Variant report

Variant	rs6968742
Chromosome Location	chr7:39649707-39649708
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C7orf11-6	chr7:39649611-39649889	ENSG00000231951.1
2	lnc-YAE1D1-1	chr7:39649086-39651687	NONHSAT120210
3	lnc-YAE1D1-1	chr7:39649316-39649879	NONHSAT120212

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10245247	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10258946	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10266149	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10486798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486800	1.00[CEU][hapmap]
rs12111908	0.98[ASN][1000 genomes]
rs17171603	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs17416652	1.00[CEU][hapmap]
rs17507685	1.00[CEU][hapmap]
rs17507748	1.00[CEU][hapmap]
rs17508696	1.00[CEU][hapmap]
rs17713754	0.82[ASN][1000 genomes]
rs17713951	0.86[ASN][1000 genomes]
rs17714049	0.98[ASN][1000 genomes]
rs17770594	0.82[ASN][1000 genomes]
rs17770612	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs17770625	0.82[ASN][1000 genomes]
rs1989533	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329455	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2329460	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2329461	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4451213	0.82[AMR][1000 genomes]
rs4469364	0.90[AFR][1000 genomes]
rs4720329	0.92[AFR][1000 genomes]
rs4723881	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4723882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723883	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723885	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58299139	0.82[ASN][1000 genomes]
rs59071947	0.82[ASN][1000 genomes]
rs61493712	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6958662	0.93[AFR][1000 genomes]
rs73375695	0.82[ASN][1000 genomes]
rs7777173	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7785964	0.82[ASN][1000 genomes]
rs7796063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7807233	1.00[CEU][hapmap]
rs7809088	0.93[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39644800-39649800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:39645200-39661600	Weak transcription	A549	lung
3	chr7:39646400-39650000	Enhancers	Stomach Mucosa	stomach
4	chr7:39647000-39649800	Enhancers	Hela-S3	cervix
5	chr7:39647600-39650000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:39647600-39650200	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr7:39647800-39649800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:39648000-39649800	Enhancers	Small Intestine	intestine
9	chr7:39648000-39649800	Enhancers	HSMM	muscle
10	chr7:39648000-39650000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr7:39648400-39651800	Flanking Active TSS	HUVEC	blood vessel
12	chr7:39648600-39649800	Enhancers	Spleen	Spleen
13	chr7:39648600-39649800	Flanking Active TSS	NH-A	brain
14	chr7:39648600-39650000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
15	chr7:39648800-39656000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr7:39649000-39649800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr7:39649000-39649800	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr7:39649000-39649800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr7:39649000-39649800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr7:39649000-39649800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr7:39649000-39649800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:39649000-39649800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr7:39649000-39649800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:39649000-39649800	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr7:39649000-39649800	Enhancers	Fetal Heart	heart
26	chr7:39649000-39649800	Active TSS	Rectal Smooth Muscle	rectum
27	chr7:39649000-39649800	Active TSS	Right Atrium	heart
28	chr7:39649000-39649800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
29	chr7:39649000-39649800	Flanking Active TSS	NHDF-Ad	bronchial
30	chr7:39649000-39650000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
31	chr7:39649000-39650000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr7:39649000-39650000	Flanking Active TSS	NHEK	skin
33	chr7:39649200-39649800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
34	chr7:39649200-39649800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr7:39649200-39649800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
36	chr7:39649200-39649800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr7:39649200-39649800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
38	chr7:39649200-39649800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
39	chr7:39649200-39649800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr7:39649200-39649800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
41	chr7:39649200-39649800	Bivalent/Poised TSS	Fetal Brain Female	brain
42	chr7:39649200-39649800	Enhancers	Placenta	Placenta
43	chr7:39649200-39649800	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr7:39649200-39649800	Flanking Active TSS	NHLF	lung
45	chr7:39649200-39650000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
46	chr7:39649200-39650000	Bivalent Enhancer	Fetal Brain Male	brain
47	chr7:39649400-39649800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr7:39649400-39649800	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr7:39649400-39649800	Bivalent/Poised TSS	Colonic Mucosa	Colon
50	chr7:39649400-39649800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach

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