Variant report

Variant	rs10242100
Chromosome Location	chr7:120983343-120983344
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120983315..120988204-chr7:120988665..120992990,4	K562	blood:
2	chr7:120983221..120985265-chr7:121035148..121036876,2	K562	blood:
3	chr7:120982229..120984096-chr7:120992298..120995156,2	K562	blood:

Variant related genes	Relation type
ENSG00000196937	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12171617	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12531355	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539772	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2536182	0.97[ASN][1000 genomes]
rs28395249	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3779381	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801382	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801383	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55963900	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56364616	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718766	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776725	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7801915	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7807953	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808155	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917726	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs917727	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1034353	chr7:120818382-121040576	Enhancers Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1026322	chr7:120841937-121188037	Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv539102	chr7:120841937-121188037	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2755350	chr7:120848049-121119049	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv2757237	chr7:120908459-120993326	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	esv2759558	chr7:120908459-120993326	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv1032054	chr7:120926379-121432971	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv539103	chr7:120926379-121432971	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Bone mineral density	24249740	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10242100	FAM3C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120970600-121016800	Weak transcription	Gastric	stomach
2	chr7:120970600-121025400	Weak transcription	Spleen	Spleen
3	chr7:120970800-121000400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:120971000-120986400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr7:120972000-120986600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:120972000-120992400	Weak transcription	Esophagus	oesophagus
7	chr7:120973800-120998800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:120974800-120986400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:120975600-120992400	Weak transcription	HSMMtube	muscle
10	chr7:120975800-120984000	Weak transcription	NHLF	lung
11	chr7:120976400-120986200	Weak transcription	NHEK	skin
12	chr7:120976400-120986800	Weak transcription	Fetal Brain Female	brain
13	chr7:120977000-120985600	Weak transcription	Left Ventricle	heart
14	chr7:120977400-120984800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr7:120977400-120987000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr7:120977600-120992400	Weak transcription	Fetal Intestine Small	intestine
17	chr7:120977800-120985800	Weak transcription	Primary T cells from cord blood	blood
18	chr7:120977800-120986600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:120977800-120999800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr7:120978000-120984000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr7:120978000-120986400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr7:120978200-120984800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr7:120978600-120986800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:120978600-120990600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr7:120978600-120994600	Weak transcription	Fetal Thymus	thymus
26	chr7:120978800-121017400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr7:120979400-120986600	Weak transcription	Fetal Muscle Leg	muscle
28	chr7:120979400-120990400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr7:120979400-120992400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr7:120979400-120992400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr7:120979400-120992400	Weak transcription	Lung	lung
32	chr7:120979400-120995400	Weak transcription	Fetal Heart	heart
33	chr7:120979600-120986800	Weak transcription	K562	blood
34	chr7:120979600-120992400	Weak transcription	Aorta	Aorta
35	chr7:120979800-120986600	Weak transcription	Colon Smooth Muscle	Colon
36	chr7:120979800-120986600	Weak transcription	HMEC	breast
37	chr7:120979800-120986800	Weak transcription	Right Ventricle	heart
38	chr7:120979800-121019400	Weak transcription	Thymus	Thymus
39	chr7:120979800-121034800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr7:120980000-120986200	Weak transcription	Fetal Intestine Large	intestine
41	chr7:120980000-120992000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr7:120980200-120986800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:120980200-120986800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr7:120980400-120984000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr7:120980400-120987200	Weak transcription	GM12878-XiMat	blood
46	chr7:120980400-120992400	Weak transcription	Fetal Stomach	stomach
47	chr7:120980400-120992600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr7:120980600-120986200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr7:120980600-120986800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr7:120980600-120990600	Weak transcription	Primary T cells fromperipheralblood	blood

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